Do 11. Sep 18:17:39 CEST 2014 /usr/local /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7737612 253704 577364 2595640 3788864 -/+ buffers/cache: 1353108 6638208 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:17:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:17:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:17:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:17:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:17:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7737324 253992 577436 2595688 3788888 -/+ buffers/cache: 1352748 6638568 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 18:17:39 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 18:27:40 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 18:27:42 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /usr/local /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat.fslregister.log Do 11. Sep 18:27:46 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/refvol.fslregister.nii... -------------------------------------- /usr/local mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /usr/local tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/reg0.13824.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/reg0.13824.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 18:27:49 CEST 2014 /usr/local flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat.fsl.mat0 Do 11. Sep 18:27:56 CEST 2014 /usr/local flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 18:27:46 CEST 2014 Ended at Do 11. Sep 18:28:08 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /usr/local mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410635300 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.467000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.386000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /usr/local mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13789/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410660289 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.393000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.509000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 18:27:42 CEST 2014 Ended at Do 11. Sep 18:28:45 CEST 2014 BBR-Run-Time-Sec 63 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 18:28:46 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo ** ERROR (nifti_image_read): failed to find header file for '/usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain' ** ERROR: nifti_image_open(/usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain): bad header info ERROR: failed to open file /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain ERROR: Could not open image /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain Image Exception : #22 :: Failed to read volume /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz terminate called after throwing an instance of 'RBD_COMMON::BaseException' Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 18:28:46 CEST 2014 New invocation of trac-all Do 11. Sep 18:47:57 CEST 2014 /usr/local /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7095712 895604 582836 2299212 3292608 -/+ buffers/cache: 1503892 6487424 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:47:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:47:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:47:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:47:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-16:47:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7097292 894024 582836 2299264 3292556 -/+ buffers/cache: 1505472 6485844 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 18:47:58 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 18:58:01 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 18:58:03 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /usr/local /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat.fslregister.log Do 11. Sep 18:58:07 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/refvol.fslregister.nii... -------------------------------------- /usr/local mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /usr/local tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/reg0.19938.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/reg0.19938.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 18:58:11 CEST 2014 /usr/local flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat.fsl.mat0 Do 11. Sep 18:58:17 CEST 2014 /usr/local flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 18:58:07 CEST 2014 Ended at Do 11. Sep 18:58:29 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /usr/local mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411037237 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.524000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.527000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /usr/local mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19901/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410977610 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.440000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.719000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 18:58:03 CEST 2014 Ended at Do 11. Sep 18:59:07 CEST 2014 BBR-Run-Time-Sec 64 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 18:59:07 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 19:00:42 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 19:04:29 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 19:04:30 CEST 2014 New invocation of trac-all Do 11. Sep 19:39:59 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1566944 6424372 664488 88996 977904 -/+ buffers/cache: 500044 7491272 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-17:39:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-17:39:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-17:39:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-17:39:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-17:39:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1588628 6402688 664404 89316 997796 -/+ buffers/cache: 501516 7489800 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 19:40:00 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 19:49:58 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 19:50:00 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat.fslregister.log Do 11. Sep 19:50:05 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/reg0.7652.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/reg0.7652.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 19:50:08 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat.fsl.mat0 Do 11. Sep 19:50:14 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 19:50:05 CEST 2014 Ended at Do 11. Sep 19:50:26 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411406846 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.410000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.302000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.7616/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411005441 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.433000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.774000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 19:50:00 CEST 2014 Ended at Do 11. Sep 19:51:09 CEST 2014 BBR-Run-Time-Sec 69 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 19:51:09 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 19:52:40 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 19:56:27 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 19:56:28 CEST 2014 New invocation of trac-all Do 11. Sep 20:00:51 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2658900 5332416 695544 754468 1372168 -/+ buffers/cache: 532264 7459052 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-18:00:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-18:00:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-18:00:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-18:00:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-18:00:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2659776 5331540 695544 754520 1372116 -/+ buffers/cache: 533140 7458176 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 20:00:52 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 20:10:50 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 20:10:51 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat.fslregister.log Do 11. Sep 20:10:56 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/reg0.13577.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/reg0.13577.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 20:10:59 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat.fsl.mat0 Do 11. Sep 20:11:06 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 20:10:56 CEST 2014 Ended at Do 11. Sep 20:11:18 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410984293 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.730000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 5.970000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.13541/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410690227 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.907000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 15.999000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 20:10:51 CEST 2014 Ended at Do 11. Sep 20:12:02 CEST 2014 BBR-Run-Time-Sec 71 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 20:12:02 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 20:13:33 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 20:17:26 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 20:17:27 CEST 2014 New invocation of trac-all Do 11. Sep 21:27:41 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3191720 4799596 704232 1249184 1381800 -/+ buffers/cache: 560736 7430580 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:27:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:27:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:27:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:27:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:27:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3193504 4797812 703668 1249240 1381180 -/+ buffers/cache: 563084 7428232 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 21:27:41 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/Cramer_Benjamin_20140905_001_031_DTI_64Ri_TE86_2x2x2_62sl_bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 21:37:38 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 21:37:39 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat.fslregister.log Do 11. Sep 21:37:44 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/reg0.19609.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/reg0.19609.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 21:37:47 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat.fsl.mat0 Do 11. Sep 21:37:54 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 21:37:44 CEST 2014 Ended at Do 11. Sep 21:38:08 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410801722 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.397000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.215000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.19573/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411408436 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.457000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.855000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 21:37:39 CEST 2014 Ended at Do 11. Sep 21:38:47 CEST 2014 BBR-Run-Time-Sec 68 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 21:38:47 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 21:40:18 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 21:44:06 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 21:44:07 CEST 2014 New invocation of trac-all Do 11. Sep 21:50:07 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3724184 4267132 711776 1751892 1389772 -/+ buffers/cache: 582520 7408796 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:50:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:50:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:50:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:50:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:50:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3725116 4266200 711776 1751944 1389720 -/+ buffers/cache: 583452 7407864 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 21:50:07 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp: cannot stat ���/media/benjamin/TOSHIBA/bvecs���: No such file or directory Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 21:50:21 CEST 2014 New invocation of trac-all Do 11. Sep 21:51:04 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3789536 4201780 728984 1797200 1406784 -/+ buffers/cache: 585552 7405764 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:51:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:51:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:51:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:51:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-19:51:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3786728 4204588 725088 1797248 1402840 -/+ buffers/cache: 586640 7404676 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 21:51:04 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 22:01:05 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 22:01:07 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat.fslregister.log Do 11. Sep 22:01:11 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/reg0.25855.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/reg0.25855.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 22:01:15 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat.fsl.mat0 Do 11. Sep 22:01:21 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 22:01:11 CEST 2014 Ended at Do 11. Sep 22:01:33 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410641232 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.435000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.128000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.25819/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410789813 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.447000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.762000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 22:01:07 CEST 2014 Ended at Do 11. Sep 22:02:11 CEST 2014 BBR-Run-Time-Sec 64 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 22:02:11 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 22:03:44 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 22:07:30 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 22:07:30 CEST 2014 New invocation of trac-all Do 11. Sep 22:26:34 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4484516 3506800 737124 2299424 1518228 -/+ buffers/cache: 666864 7324452 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:26:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:26:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:26:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:26:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:26:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4484764 3506552 737124 2299476 1518176 -/+ buffers/cache: 667112 7324204 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 22:26:34 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 22:36:31 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 22:36:33 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat.fslregister.log Do 11. Sep 22:36:37 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/reg0.32210.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/reg0.32210.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 22:36:40 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat.fsl.mat0 Do 11. Sep 22:36:47 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 22:36:37 CEST 2014 Ended at Do 11. Sep 22:36:58 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410491635 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.408000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.066000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.32174/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410896300 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.448000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.758000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 22:36:33 CEST 2014 Ended at Do 11. Sep 22:37:37 CEST 2014 BBR-Run-Time-Sec 64 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 22:37:37 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 22:39:12 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 22:42:57 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 22:42:58 CEST 2014 New invocation of trac-all Do 11. Sep 22:58:57 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5376420 2614896 713088 2851136 1771972 -/+ buffers/cache: 753312 7238004 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:58:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:58:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:58:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:58:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-20:58:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5377084 2614232 713080 2851184 1771896 -/+ buffers/cache: 754004 7237312 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 22:58:57 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 23:08:54 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 23:08:56 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat.fslregister.log Do 11. Sep 23:09:01 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/reg0.6174.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/reg0.6174.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 23:09:04 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat.fsl.mat0 Do 11. Sep 23:09:10 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 23:09:01 CEST 2014 Ended at Do 11. Sep 23:09:22 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410971017 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.415000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.038000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.6138/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411053003 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.476000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 19.679000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 23:08:56 CEST 2014 Ended at Do 11. Sep 23:10:05 CEST 2014 BBR-Run-Time-Sec 69 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 23:10:05 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 23:11:38 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 23:15:27 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 23:15:28 CEST 2014 New invocation of trac-all Do 11. Sep 23:29:27 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5883840 2107476 702336 3346564 1769140 -/+ buffers/cache: 768136 7223180 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-21:29:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-21:29:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-21:29:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-21:29:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-21:29:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5885140 2106176 702316 3346616 1769072 -/+ buffers/cache: 769452 7221864 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Do 11. Sep 23:29:27 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 67 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Do 11. Sep 23:39:28 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Do 11. Sep 23:39:30 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat.fslregister.log Do 11. Sep 23:39:35 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/reg0.12164.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/reg0.12164.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Do 11. Sep 23:39:38 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat.fsl.mat0 Do 11. Sep 23:39:45 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Do 11. Sep 23:39:35 CEST 2014 Ended at Do 11. Sep 23:39:57 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410568932 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.753000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 5.393000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.12124/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410657760 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.916000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 16.173000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Do 11. Sep 23:39:30 CEST 2014 Ended at Do 11. Sep 23:40:40 CEST 2014 BBR-Run-Time-Sec 70 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Do 11. Sep 23:40:40 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Do 11. Sep 23:42:12 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Do 11. Sep 23:46:11 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Do 11. Sep 23:46:11 CEST 2014 New invocation of trac-all Fr 12. Sep 00:51:12 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7275588 715728 785180 3955112 2222172 -/+ buffers/cache: 1098304 6893012 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:51:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:51:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:51:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:51:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:51:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7275936 715380 785180 3955164 2222120 -/+ buffers/cache: 1098652 6892664 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 00:51:13 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp: cannot stat ���/media/benjamin/TOSHIBA/bvecs���: No such file or directory Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 00:51:26 CEST 2014 New invocation of trac-all Fr 12. Sep 00:52:22 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7321024 670292 783376 4000392 2220296 -/+ buffers/cache: 1100336 6890980 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:52:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:52:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:52:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:52:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/11-22:52:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 7321932 669384 783376 4000444 2220244 -/+ buffers/cache: 1101244 6890072 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 00:52:22 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvec /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bval /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Fr 12. Sep 01:02:21 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Fr 12. Sep 01:02:23 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat.fslregister.log Fr 12. Sep 01:02:28 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/reg0.21218.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/reg0.21218.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Fr 12. Sep 01:02:31 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat.fsl.mat0 Fr 12. Sep 01:02:38 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Fr 12. Sep 01:02:28 CEST 2014 Ended at Fr 12. Sep 01:02:49 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410530903 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.532000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.622000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.21182/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1410505832 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 3.718000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 16.959000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Fr 12. Sep 01:02:23 CEST 2014 Ended at Fr 12. Sep 01:03:36 CEST 2014 BBR-Run-Time-Sec 73 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Fr 12. Sep 01:03:36 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Fr 12. Sep 01:05:09 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fr 12. Sep 01:09:16 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 01:09:17 CEST 2014 New invocation of trac-all Fr 12. Sep 12:09:54 CEST 2014 /media/benjamin/TOSHIBA /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1806060 6185256 318188 50664 969944 -/+ buffers/cache: 785452 7205864 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:09:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:09:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:09:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:09:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:09:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1826784 6164532 318188 50980 990244 -/+ buffers/cache: 785560 7205756 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 12:09:55 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz New invocation of trac-all Fr 12. Sep 12:10:44 CEST 2014 /media/benjamin/TOSHIBA /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2265420 5725896 318532 296364 1179992 -/+ buffers/cache: 789064 7202252 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:10:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:10:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:10:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:10:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:10:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2265828 5725488 318684 296428 1180080 -/+ buffers/cache: 789320 7201996 Swap: 0 0 0 New invocation of trac-all Fr 12. Sep 12:11:09 CEST 2014 /media/benjamin/TOSHIBA /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2258528 5732788 312700 296436 1174180 -/+ buffers/cache: 787912 7203404 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2257972 5733344 310900 296488 1172328 -/+ buffers/cache: 789156 7202160 Swap: 0 0 0 New invocation of trac-all Fr 12. Sep 12:11:18 CEST 2014 /media/benjamin/TOSHIBA /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2256716 5734600 310288 296492 1171772 -/+ buffers/cache: 788452 7202864 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:11:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2257716 5733600 310396 296568 1171876 -/+ buffers/cache: 789272 7202044 Swap: 0 0 0 New invocation of trac-all Fr 12. Sep 12:15:35 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2272460 5718856 308572 297008 1169280 -/+ buffers/cache: 806172 7185144 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:15:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:15:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:15:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:15:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:15:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2274508 5716808 309396 297060 1170056 -/+ buffers/cache: 807392 7183924 Swap: 0 0 0 New invocation of trac-all Fr 12. Sep 12:16:52 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2276160 5715156 307516 297076 1168192 -/+ buffers/cache: 810892 7180424 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:16:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:16:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:16:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:16:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:16:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 2276488 5714828 307808 297128 1168432 -/+ buffers/cache: 810928 7180388 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 12:16:53 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Fr 12. Sep 12:26:56 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Fr 12. Sep 12:26:58 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat.fslregister.log Fr 12. Sep 12:27:02 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/reg0.8997.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/reg0.8997.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Fr 12. Sep 12:27:05 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat.fsl.mat0 Fr 12. Sep 12:27:12 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Fr 12. Sep 12:27:02 CEST 2014 Ended at Fr 12. Sep 12:27:24 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411044485 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.457000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.235000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.8961/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411357952 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.460000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.313000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Fr 12. Sep 12:26:58 CEST 2014 Ended at Fr 12. Sep 12:28:03 CEST 2014 BBR-Run-Time-Sec 65 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Fr 12. Sep 12:28:03 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Fr 12. Sep 12:29:34 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fr 12. Sep 12:33:18 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 12:33:19 CEST 2014 New invocation of trac-all Fr 12. Sep 12:40:53 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3298848 4692468 481672 849376 1537056 -/+ buffers/cache: 912416 7078900 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:40:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:40:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:40:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:40:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-10:40:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 3299988 4691328 481672 849424 1537008 -/+ buffers/cache: 913556 7077760 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 12:40:54 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/bvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/bvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Fr 12. Sep 12:50:52 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Fr 12. Sep 12:50:55 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat.fslregister.log Fr 12. Sep 12:51:01 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/reg0.15075.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/reg0.15075.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Fr 12. Sep 12:51:04 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat.fsl.mat0 Fr 12. Sep 12:51:10 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Fr 12. Sep 12:51:01 CEST 2014 Ended at Fr 12. Sep 12:51:22 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411326401 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.532000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.635000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.15033/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411345765 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.588000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.599000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Fr 12. Sep 12:50:55 CEST 2014 Ended at Fr 12. Sep 12:52:01 CEST 2014 BBR-Run-Time-Sec 66 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Fr 12. Sep 12:52:01 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Fr 12. Sep 12:53:33 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fr 12. Sep 12:57:20 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 12:57:21 CEST 2014 New invocation of trac-all Fr 12. Sep 14:03:59 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4111132 3880184 521048 1361004 1730016 -/+ buffers/cache: 1020112 6971204 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:03:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:03:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:03:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:03:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:03:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4112160 3879156 521048 1361056 1729964 -/+ buffers/cache: 1021140 6970176 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 14:03:59 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/new_vecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/new_vals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz niiRead(): error opening file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 14:13:52 CEST 2014 New invocation of trac-all Fr 12. Sep 14:26:30 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4406216 3585100 525140 1628632 1740204 -/+ buffers/cache: 1037380 6953936 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:26:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:26:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:26:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:26:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:26:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4406388 3584928 524988 1628684 1740024 -/+ buffers/cache: 1037680 6953636 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 14:26:31 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/newvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/newvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz niiRead(): error opening file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 14:36:31 CEST 2014 New invocation of trac-all Fr 12. Sep 14:40:58 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4694784 3296532 526604 1897568 1747844 -/+ buffers/cache: 1049372 6941944 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:40:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:40:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:40:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:40:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:40:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 4695288 3296028 526780 1897616 1748020 -/+ buffers/cache: 1049652 6941664 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 14:40:58 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /media/benjamin/TOSHIBA/newvecs.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /media/benjamin/TOSHIBA/newvals.txt /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz niiRead(): error opening file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 14:50:54 CEST 2014 New invocation of trac-all Fr 12. Sep 14:54:32 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5005308 2986008 537316 2163516 1760348 -/+ buffers/cache: 1081444 6909872 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:54:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:54:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:54:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:54:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-12:54:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5005692 2985624 536976 2163564 1759960 -/+ buffers/cache: 1082168 6909148 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 14:54:32 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /home/benjamin/Downloads/newvec /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /home/benjamin/Downloads/newvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz niiRead(): error opening file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 15:04:25 CEST 2014 New invocation of trac-all Fr 12. Sep 15:06:18 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5261932 2729384 522584 2429048 1746052 -/+ buffers/cache: 1086832 6904484 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:06:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:06:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:06:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:06:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:06:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5262356 2728960 522584 2429100 1746004 -/+ buffers/cache: 1087252 6904064 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 15:06:18 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /home/benjamin/Downloads/newvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /home/benjamin/Downloads/newvec /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz niiRead(): error opening file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 15:16:11 CEST 2014 New invocation of trac-all Fr 12. Sep 15:24:55 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5552972 2438344 530752 2694996 1755340 -/+ buffers/cache: 1102636 6888680 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:24:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:24:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:24:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:24:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-13:24:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 5553380 2437936 530752 2695048 1755288 -/+ buffers/cache: 1103044 6888272 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 15:24:55 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz niiRead(): error opening file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame.nii.gz Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 15:34:54 CEST 2014 New invocation of trac-all Fr 12. Sep 18:28:36 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1072164 6919152 272784 39412 569608 -/+ buffers/cache: 463144 7528172 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:28:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:28:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:28:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:28:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:28:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1092996 6898320 273124 40056 589632 -/+ buffers/cache: 463308 7528008 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 18:28:37 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 New invocation of trac-all Fr 12. Sep 18:37:14 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1710572 6280744 284336 373492 839900 -/+ buffers/cache: 497180 7494136 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1710508 6280808 284336 373544 839864 -/+ buffers/cache: 497100 7494216 Swap: 0 0 0 New invocation of trac-all Fr 12. Sep 18:37:31 CEST 2014 /home/benjamin /usr/local/freesurfer/bin/trac-all -prep -c /media/benjamin/TOSHIBA/Tinnitus/Studie1/dmrirc.test Subject Proband13_MPRAGE SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1704300 6287016 276952 373552 832612 -/+ buffers/cache: 498136 7493180 Swap: 0 0 0 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/12-16:37:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: benjamin Machine: benjamin-ThinkPad-T530 Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc benjamin benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 61655 maxlocks unlimited maxsignal 61655 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 7991316 1705100 6286216 276952 373604 832560 -/+ buffers/cache: 498936 7492380 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fr 12. Sep 18:37:31 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 70 files in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031 INFO: Scanning for Series Number 31 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 863.4529 894.5696 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (106 106 62), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9600, TR = 9600 ms PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13/Proband13_MRT/FORSCHUNG_PSYCHIATRIE_20140905_103030_418000/DTI_64RI_TE86_2X2X2_62SL_0031/CRAMER_BENJAMIN.MR.FORSCHUNG_PSYCHIATRIE.0031.0001.2014.09.05.11.42.39.304171.14498929.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Cramer^Benjamin Date and time StudyDate 20140905 StudyTime 103030.418000 SeriesTime 113256.647000 AcqTime 112936.590000 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64Ri_TE86_2x2x2_62sl PhEncDir ROW EchoNo 1 FlipAngle 90 EchoTime 86 InversionTime -1 RepetitionTime 9600 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 848 NImageCols 848 NFrames 65 SliceArraylSize 62 IsMosaic 1 ImgPos 107.4529 138.5695 -0.6196 VolRes 2.0377 2.0377 2.0000 VolDim 106 106 62 Vc -1.0000 -0.0000 0.0000 Vr 0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.5471 30.5695 61.3804 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9600.00, TE=86.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (2.05103e-10, -1, 0) k_ras = (-0, -0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz... cp /home/benjamin/Downloads/newvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs cp /home/benjamin/Downloads/newvec /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.30474 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.nii.gz x -y z /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.mghdti.bvals /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals eddy_correct /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_orig_flip.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz 0 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0000 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0001 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0002 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0003 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0004 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0005 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0006 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0007 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0008 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0009 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0010 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0011 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0012 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0013 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0014 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0015 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0016 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0017 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0018 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0019 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0020 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0021 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0022 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0023 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0024 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0025 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0026 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0027 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0028 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0029 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0030 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0031 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0032 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0033 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0034 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0035 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0036 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0037 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0038 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0039 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0040 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0041 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0042 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0043 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0044 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0045 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0046 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0047 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0048 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0049 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0050 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0051 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0052 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0053 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0054 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0055 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0056 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0057 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0058 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0059 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0060 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0061 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0062 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0063 processing /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_tmp0064 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot xfmrot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.ecclog /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs.norot /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/data.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz... mri_concat --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_frame0.nii.gz --mean --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz bet /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff #------------------------------------- #@# Intra-subject registration Fr 12. Sep 18:47:29 CEST 2014 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brain.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz... flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz --targ /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.log Fr 12. Sep 18:47:31 CEST 2014 setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin /usr/local/freesurfer/bin/bbregister --s Proband13_MPRAGE --init-fsl --dti --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --fslmat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii... fslregister --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister --dof 6 --fsvol brainmask.mgz Log file is /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat.fslregister.log Fr 12. Sep 18:47:35 CEST 2014 --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ benjamin-ThinkPad-T530 Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/refvol.fslregister.nii mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/refvol.fslregister.nii... -------------------------------------- /home/benjamin mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.05103e-10, 0) j_ras = (-2.05103e-10, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii... Mov determinant is -8.30474 /home/benjamin tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/reg0.11495.dat --regheader --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat.fsl.mat0 --s Proband13_MPRAGE --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/reg0.11495.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 0.000 0.000 -1.807; 0.000 0.000 1.000 -50.451; 0.000 -1.000 0.000 -1.939; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8.30474, ref det = -1 Fr 12. Sep 18:47:38 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/4.1/etc/flirtsch/xyztrans.sch -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat.fsl.mat0 Fr 12. Sep 18:47:45 CEST 2014 /home/benjamin flirt.fsl -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/refvol.fslregister.nii -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat.fsl.mat -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Proband13_MPRAGE --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat --fslreg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 -0.002 0.018 17.184; 0.018 -0.020 -1.000 140.334; 0.003 1.000 -0.020 18.090; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8.30474, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Determinant 1 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P (standard_in) 1: illegal character: M (standard_in) 1: illegal character: P (standard_in) 1: illegal character: R (standard_in) 1: syntax error (standard_in) 1: illegal character: G Started at Fr 12. Sep 18:47:35 CEST 2014 Ended at Fr 12. Sep 18:47:57 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat --surf orig mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.init.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411281101 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.973444 1 -25.0 -25.0 25.0 0.974336 2 -25.0 25.0 -25.0 1.003478 3 -25.0 25.0 25.0 0.989896 4 25.0 -25.0 -25.0 0.982863 5 25.0 -25.0 25.0 0.993231 6 25.0 25.0 -25.0 0.998223 7 25.0 25.0 25.0 0.996063 REL: 8 0.156701 7.911535 0.988942 rel = 0.158453 Initial costs ---------------- Number of surface hits 3256 WM Intensity 334.0617 +/- 144.0687 Ctx Intensity 454.3987 +/- 204.6286 Pct Contrast 29.4198 +/- 22.8484 Cost 0.1567 RelCost 0.1585 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9824 0.9824 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9708 0.9708 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.8511 0.8511 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8165 0.8165 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8110 0.8110 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8087 0.8087 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.8082 0.8082 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7600 0.7600 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7596 0.7596 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6789 0.6789 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.6387 0.6387 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5982 0.5982 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1567 0.1567 0.0 Brute Force -------------------------- Min cost was 0.156701 Number of iterations 729 Search time 1.491000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.174 0.000 0.000 0.000 0.000 0.000 0.1544843746 8 0.170 0.000 0.000 0.000 0.000 0.000 0.1544614847 11 0.166 0.000 0.000 0.000 0.000 0.000 0.1544583863 21 0.166 0.044 0.000 0.000 0.000 0.000 0.1534122269 28 0.166 0.047 0.000 0.000 0.000 0.000 0.1534022334 38 0.166 0.047 0.039 0.000 0.000 0.000 0.1527832398 41 0.166 0.047 0.040 0.000 0.000 0.000 0.1527830017 49 0.166 0.047 0.040 -0.262 0.000 0.000 0.1441629220 51 0.166 0.047 0.040 -0.198 0.000 0.000 0.1431666997 52 0.166 0.047 0.040 -0.199 0.000 0.000 0.1431483391 53 0.166 0.047 0.040 -0.214 0.000 0.000 0.1430693011 55 0.166 0.047 0.040 -0.211 0.000 0.000 0.1430609176 56 0.166 0.047 0.040 -0.210 0.000 0.000 0.1430605932 64 0.166 0.047 0.040 -0.210 0.155 0.000 0.1398023025 66 0.166 0.047 0.040 -0.210 0.115 0.000 0.1395332750 68 0.166 0.047 0.040 -0.210 0.126 0.000 0.1394526495 76 0.166 0.047 0.040 -0.210 0.126 0.382 0.1384862997 77 0.166 0.047 0.040 -0.210 0.126 0.204 0.1365040360 79 0.166 0.047 0.040 -0.210 0.126 0.126 0.1363026869 80 0.166 0.047 0.040 -0.210 0.126 0.142 0.1362565524 81 0.166 0.047 0.040 -0.210 0.126 0.151 0.1362299791 82 0.166 0.047 0.040 -0.210 0.126 0.171 0.1361995250 95 0.119 0.047 0.040 -0.210 0.126 0.171 0.1361084886 96 0.139 0.047 0.040 -0.210 0.126 0.171 0.1360653631 98 0.150 0.047 0.040 -0.210 0.126 0.171 0.1360568054 99 0.148 0.047 0.040 -0.210 0.126 0.171 0.1360539680 100 0.146 0.047 0.040 -0.210 0.126 0.171 0.1360533879 101 0.145 0.047 0.040 -0.210 0.126 0.171 0.1360533349 109 0.145 -0.097 0.040 -0.210 0.126 0.171 0.1353455948 112 0.145 -0.166 0.040 -0.210 0.126 0.171 0.1351644897 114 0.145 -0.145 0.040 -0.210 0.126 0.171 0.1351006442 115 0.145 -0.143 0.040 -0.210 0.126 0.171 0.1350994364 116 0.145 -0.141 0.040 -0.210 0.126 0.171 0.1350991469 118 0.145 -0.142 0.040 -0.210 0.126 0.171 0.1350991391 125 0.145 -0.142 0.056 -0.210 0.126 0.171 0.1349595766 126 0.145 -0.142 0.075 -0.210 0.126 0.171 0.1348201292 130 0.145 -0.142 0.086 -0.210 0.126 0.171 0.1347813133 131 0.145 -0.142 0.088 -0.210 0.126 0.171 0.1347791409 132 0.145 -0.142 0.091 -0.210 0.126 0.171 0.1347790525 135 0.145 -0.142 0.090 -0.210 0.126 0.171 0.1347788907 142 0.145 -0.142 0.090 -0.337 0.126 0.171 0.1317724507 143 0.145 -0.142 0.090 -0.355 0.126 0.171 0.1317178714 144 0.145 -0.142 0.090 -0.357 0.126 0.171 0.1317096966 147 0.145 -0.142 0.090 -0.383 0.126 0.171 0.1316652098 149 0.145 -0.142 0.090 -0.374 0.126 0.171 0.1316429416 150 0.145 -0.142 0.090 -0.375 0.126 0.171 0.1316424418 151 0.145 -0.142 0.090 -0.376 0.126 0.171 0.1316423325 163 0.145 -0.142 0.090 -0.376 0.106 0.171 0.1315631805 164 0.145 -0.142 0.090 -0.376 0.109 0.171 0.1315540338 165 0.145 -0.142 0.090 -0.376 0.112 0.171 0.1315503524 175 0.145 -0.142 0.090 -0.376 0.112 0.216 0.1315305805 177 0.145 -0.142 0.090 -0.376 0.112 0.242 0.1315159714 178 0.145 -0.142 0.090 -0.376 0.112 0.243 0.1315156535 189 0.139 -0.142 0.090 -0.376 0.112 0.243 0.1313867955 191 0.087 -0.142 0.090 -0.376 0.112 0.243 0.1312610877 192 0.110 -0.142 0.090 -0.376 0.112 0.243 0.1310730369 193 0.111 -0.142 0.090 -0.376 0.112 0.243 0.1310727908 201 0.111 -0.154 0.090 -0.376 0.112 0.243 0.1308285315 202 0.111 -0.305 0.090 -0.376 0.112 0.243 0.1303002256 204 0.111 -0.246 0.090 -0.376 0.112 0.243 0.1301918741 205 0.111 -0.260 0.090 -0.376 0.112 0.243 0.1301428720 206 0.111 -0.268 0.090 -0.376 0.112 0.243 0.1301102425 207 0.111 -0.282 0.090 -0.376 0.112 0.243 0.1300791578 218 0.111 -0.282 0.074 -0.376 0.112 0.243 0.1300551878 219 0.111 -0.282 0.076 -0.376 0.112 0.243 0.1300537294 228 0.111 -0.282 0.076 -0.391 0.112 0.243 0.1300185211 229 0.111 -0.282 0.076 -0.390 0.112 0.243 0.1300171232 230 0.111 -0.282 0.076 -0.388 0.112 0.243 0.1300153390 232 0.111 -0.282 0.076 -0.387 0.112 0.243 0.1300152947 242 0.111 -0.282 0.076 -0.387 0.110 0.243 0.1300130560 243 0.111 -0.282 0.076 -0.387 0.108 0.243 0.1300115011 255 0.111 -0.282 0.076 -0.387 0.108 0.222 0.1299646979 256 0.111 -0.282 0.076 -0.387 0.108 0.221 0.1299643551 257 0.111 -0.282 0.076 -0.387 0.108 0.219 0.1299641502 259 0.111 -0.282 0.076 -0.387 0.108 0.218 0.1299640557 270 0.113 -0.282 0.076 -0.387 0.108 0.218 0.1299634785 281 0.113 -0.283 0.076 -0.387 0.108 0.218 0.1299622708 283 0.113 -0.285 0.076 -0.387 0.108 0.218 0.1299613242 284 0.113 -0.286 0.076 -0.387 0.108 0.218 0.1299611064 292 0.113 -0.286 0.081 -0.387 0.108 0.218 0.1299532006 293 0.113 -0.286 0.084 -0.387 0.108 0.218 0.1299479922 297 0.113 -0.286 0.086 -0.387 0.108 0.218 0.1299467333 298 0.113 -0.286 0.087 -0.387 0.108 0.218 0.1299467093 307 0.113 -0.286 0.087 -0.391 0.108 0.218 0.1299347760 308 0.113 -0.286 0.087 -0.395 0.108 0.218 0.1299342607 309 0.113 -0.286 0.087 -0.393 0.108 0.218 0.1299336277 319 0.113 -0.286 0.087 -0.393 0.115 0.218 0.1299240284 320 0.113 -0.286 0.087 -0.393 0.116 0.218 0.1299239449 329 0.113 -0.286 0.087 -0.393 0.116 0.222 0.1299149712 330 0.113 -0.286 0.087 -0.393 0.116 0.229 0.1299139324 332 0.113 -0.286 0.087 -0.393 0.116 0.226 0.1299136778 333 0.113 -0.286 0.087 -0.393 0.116 0.227 0.1299136541 335 0.115 -0.290 0.098 -0.400 0.123 0.236 0.1299002226 368 0.114 -0.291 0.093 -0.393 0.116 0.227 0.1298976906 369 0.114 -0.291 0.092 -0.393 0.116 0.227 0.1298974984 379 0.114 -0.291 0.092 -0.399 0.116 0.227 0.1298887213 380 0.114 -0.291 0.092 -0.398 0.116 0.227 0.1298884412 390 0.114 -0.291 0.092 -0.398 0.113 0.227 0.1298835474 402 0.114 -0.291 0.092 -0.398 0.113 0.234 0.1298739486 405 0.116 -0.295 0.096 -0.403 0.110 0.241 0.1298717497 414 0.119 -0.291 0.092 -0.398 0.113 0.234 0.1298671900 427 0.119 -0.293 0.092 -0.398 0.113 0.234 0.1298643387 428 0.119 -0.294 0.092 -0.398 0.113 0.234 0.1298637667 437 0.119 -0.294 0.100 -0.398 0.113 0.234 0.1298554392 448 0.119 -0.294 0.100 -0.402 0.113 0.234 0.1298442941 459 0.119 -0.294 0.100 -0.402 0.112 0.234 0.1298420960 460 0.119 -0.294 0.100 -0.402 0.108 0.234 0.1298375842 462 0.119 -0.294 0.100 -0.402 0.106 0.234 0.1298370403 472 0.119 -0.294 0.100 -0.402 0.106 0.235 0.1298354624 474 0.119 -0.294 0.100 -0.402 0.106 0.236 0.1298351792 484 0.126 -0.294 0.100 -0.402 0.106 0.236 0.1298184156 496 0.126 -0.287 0.100 -0.402 0.106 0.236 0.1298128422 498 0.126 -0.289 0.100 -0.402 0.106 0.236 0.1298118229 499 0.126 -0.290 0.100 -0.402 0.106 0.236 0.1298115100 508 0.126 -0.290 0.104 -0.402 0.106 0.236 0.1297984105 509 0.126 -0.290 0.112 -0.402 0.106 0.236 0.1297858982 520 0.126 -0.290 0.112 -0.403 0.106 0.236 0.1297848290 521 0.126 -0.290 0.112 -0.404 0.106 0.236 0.1297843449 533 0.126 -0.290 0.112 -0.404 0.104 0.236 0.1297837528 536 0.126 -0.290 0.112 -0.404 0.105 0.236 0.1297832464 546 0.126 -0.290 0.112 -0.404 0.105 0.237 0.1297830058 557 0.134 -0.290 0.112 -0.404 0.105 0.237 0.1297667045 561 0.133 -0.290 0.112 -0.404 0.105 0.237 0.1297661001 574 0.133 -0.282 0.112 -0.404 0.105 0.237 0.1297627709 575 0.133 -0.284 0.112 -0.404 0.105 0.237 0.1297614115 576 0.133 -0.285 0.112 -0.404 0.105 0.237 0.1297613729 587 0.133 -0.285 0.116 -0.404 0.105 0.237 0.1297546827 589 0.133 -0.285 0.117 -0.404 0.105 0.237 0.1297545604 600 0.133 -0.285 0.117 -0.401 0.105 0.237 0.1297529501 601 0.133 -0.285 0.117 -0.402 0.105 0.237 0.1297527339 610 0.133 -0.285 0.117 -0.402 0.104 0.237 0.1297522804 620 0.133 -0.285 0.117 -0.402 0.104 0.234 0.1297517843 623 0.139 -0.280 0.123 -0.400 0.103 0.232 0.1297350351 626 0.150 -0.272 0.131 -0.397 0.101 0.228 0.1297277593 627 0.148 -0.274 0.130 -0.398 0.101 0.229 0.1297271732 632 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297270651 633 0.147 -0.274 0.129 -0.398 0.101 0.229 0.1297270403 634 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297269256 635 0.148 -0.274 0.129 -0.398 0.101 0.229 0.1297268276 647 0.148 -0.274 0.129 -0.398 0.101 0.230 0.1297267231 656 0.148 -0.256 0.129 -0.398 0.101 0.230 0.1296949809 658 0.148 -0.244 0.129 -0.398 0.101 0.230 0.1296835203 659 0.148 -0.246 0.129 -0.398 0.101 0.230 0.1296820348 660 0.148 -0.248 0.129 -0.398 0.101 0.230 0.1296816594 661 0.148 -0.249 0.129 -0.398 0.101 0.230 0.1296814584 677 0.148 -0.249 0.130 -0.398 0.101 0.230 0.1296813801 687 0.148 -0.249 0.130 -0.367 0.101 0.230 0.1296738861 689 0.148 -0.249 0.130 -0.382 0.101 0.230 0.1296009611 701 0.148 -0.249 0.130 -0.382 0.100 0.230 0.1295981392 702 0.148 -0.249 0.130 -0.382 0.099 0.230 0.1295976240 705 0.154 -0.244 0.135 -0.380 0.098 0.228 0.1295638625 710 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636814 711 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636689 712 0.155 -0.243 0.136 -0.380 0.098 0.227 0.1295636606 724 0.155 -0.243 0.136 -0.380 0.098 0.233 0.1295517670 726 0.155 -0.243 0.136 -0.380 0.098 0.236 0.1295489200 727 0.155 -0.243 0.136 -0.380 0.098 0.237 0.1295481760 737 0.155 -0.244 0.136 -0.380 0.098 0.237 0.1295478828 748 0.155 -0.244 0.131 -0.380 0.098 0.237 0.1295454094 749 0.155 -0.244 0.133 -0.380 0.098 0.237 0.1295445884 770 0.155 -0.244 0.133 -0.380 0.096 0.237 0.1295426400 771 0.155 -0.244 0.133 -0.380 0.095 0.237 0.1295423118 778 0.158 -0.242 0.135 -0.379 0.095 0.236 0.1295407743 779 0.157 -0.243 0.134 -0.380 0.095 0.236 0.1295400541 783 0.156 -0.243 0.134 -0.380 0.095 0.236 0.1295399509 798 0.156 -0.243 0.134 -0.380 0.095 0.238 0.1295391954 819 0.156 -0.243 0.131 -0.380 0.095 0.238 0.1295382499 820 0.156 -0.243 0.132 -0.380 0.095 0.238 0.1295376514 842 0.156 -0.243 0.132 -0.380 0.094 0.238 0.1295374057 851 0.158 -0.242 0.133 -0.379 0.094 0.237 0.1295367017 852 0.157 -0.242 0.133 -0.379 0.094 0.237 0.1295365371 854 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295365016 856 0.157 -0.242 0.133 -0.379 0.094 0.238 0.1295364777 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.963372 1 -25.0 -25.0 25.0 0.970049 2 -25.0 25.0 -25.0 1.006685 3 -25.0 25.0 25.0 0.999762 4 25.0 -25.0 -25.0 0.971089 5 25.0 -25.0 25.0 1.002195 6 25.0 25.0 -25.0 1.014738 7 25.0 25.0 25.0 1.002292 REL: 8 0.129536 7.930182 0.991273 rel = 0.130677 Number of iterations 10 Min cost was 0.129536 Number of FunctionCalls 860 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.567000 sec Parameters at optimum (transmm) 0.15731 -0.24247 0.13258 Parameters at optimum (rotdeg) -0.37932 0.09394 0.23751 Final costs ---------------- Number of surface hits 3255 WM Intensity 330.4544 +/- 138.0509 Ctx Intensity 450.5762 +/- 191.1107 Pct Contrast 29.9727 +/- 21.9122 Cost 0.1295 RelCost 0.1585 Reg at min cost was 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.003 0.018 -2.865; -0.018 -0.020 1.000 -49.931; -0.002 -1.000 -0.020 -1.890; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.002 0.004 -0.362; -0.004 0.007 0.000 0.265; 0.002 -0.000 0.007 -0.468; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.525788 Computing change in rh position Surface RMS Diff (mm) 0.471158 0.974431 mri_segreg done mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 cd /home/benjamin mri_segreg --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii --init-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/bbr.pass1.dat --out-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin movvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/template.nii regfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/tmp.bbregister.11459/bbr.pass1.dat subject Proband13_MPRAGE dof 6 outregfile /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1411470736 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.982989 1 -25.0 -25.0 25.0 0.975688 2 -25.0 25.0 -25.0 0.970230 3 -25.0 25.0 25.0 0.990568 4 25.0 -25.0 -25.0 0.982591 5 25.0 -25.0 25.0 0.993239 6 25.0 25.0 -25.0 0.982028 7 25.0 25.0 25.0 1.005993 REL: 8 0.152765 7.883325 0.985416 rel = 0.155026 Initial costs ---------------- Number of surface hits 325469 WM Intensity 327.7112 +/- 137.0825 Ctx Intensity 445.3865 +/- 191.6618 Pct Contrast 29.5347 +/- 22.4520 Cost 0.1528 RelCost 0.1550 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1408 0.1408 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1382 0.1382 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1357 0.1357 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1343 0.1343 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1343 0.1343 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1331 0.1331 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1325 0.1325 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1325 0.1325 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1319 0.1319 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1310 0.1310 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.1305 0.1305 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1304 0.1304 0.0 336 0.0000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1301 0.1301 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1295 0.1295 0.0 Brute Force -------------------------- Min cost was 0.129536 Number of iterations 729 Search time 1.566000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.109 0.000 0.000 0.000 0.000 0.000 0.1519113729 8 0.106 0.000 0.000 0.000 0.000 0.000 0.1519070930 9 0.097 0.000 0.000 0.000 0.000 0.000 0.1518975410 13 0.096 0.000 0.000 0.000 0.000 0.000 0.1518973704 21 0.096 0.057 0.000 0.000 0.000 0.000 0.1516017312 22 0.096 0.056 0.000 0.000 0.000 0.000 0.1516016462 30 0.096 0.056 -0.034 0.000 0.000 0.000 0.1514489297 31 0.096 0.056 -0.033 0.000 0.000 0.000 0.1514481249 32 0.096 0.056 -0.031 0.000 0.000 0.000 0.1514477305 35 0.096 0.056 -0.032 0.000 0.000 0.000 0.1514477297 42 0.096 0.056 -0.032 0.076 0.000 0.000 0.1510013437 44 0.096 0.056 -0.032 0.074 0.000 0.000 0.1510009541 54 0.096 0.056 -0.032 0.074 0.058 0.000 0.1505618427 55 0.096 0.056 -0.032 0.074 0.063 0.000 0.1505575220 56 0.096 0.056 -0.032 0.074 0.065 0.000 0.1505564883 65 0.096 0.056 -0.032 0.074 0.065 0.063 0.1503672112 67 0.096 0.056 -0.032 0.074 0.065 0.077 0.1503593819 72 0.096 0.056 -0.032 0.074 0.065 0.078 0.1503593749 82 0.098 0.056 -0.032 0.074 0.065 0.078 0.1503591699 92 0.098 0.066 -0.032 0.074 0.065 0.078 0.1503513179 93 0.098 0.065 -0.032 0.074 0.065 0.078 0.1503484275 104 0.098 0.065 -0.033 0.074 0.065 0.078 0.1503484203 127 0.098 0.065 -0.033 0.074 0.057 0.078 0.1503388377 128 0.098 0.065 -0.033 0.074 0.056 0.078 0.1503385587 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.982194 1 -25.0 -25.0 25.0 0.977977 2 -25.0 25.0 -25.0 0.970444 3 -25.0 25.0 25.0 0.991477 4 25.0 -25.0 -25.0 0.981964 5 25.0 -25.0 25.0 0.993690 6 25.0 25.0 -25.0 0.982769 7 25.0 25.0 25.0 1.006655 REL: 8 0.150339 7.887170 0.985896 rel = 0.152489 Number of iterations 2 Min cost was 0.150339 Number of FunctionCalls 201 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.484000 sec Parameters at optimum (transmm) 0.09792 0.06477 -0.03335 Parameters at optimum (rotdeg) 0.07408 0.05551 0.07822 Final costs ---------------- Number of surface hits 325510 WM Intensity 328.0973 +/- 137.7961 Ctx Intensity 446.7206 +/- 193.0876 Pct Contrast 29.7149 +/- 22.3605 Cost 0.1503 RelCost 0.1550 Reg at min cost was 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Writing optimal reg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 1.000 -0.004 0.013 -2.503; -0.014 -0.027 1.000 -50.196; -0.004 -1.000 -0.027 -1.422; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 0.001 -0.165; -0.001 -0.001 -0.000 -0.063; 0.001 0.000 -0.001 0.096; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.144898 Computing change in rh position Surface RMS Diff (mm) 0.165010 0.276239 mri_segreg done tkregister2_cmdl --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz reg file /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz Tmov: -------------------- -2.038 0.000 0.000 108.000; 0.000 0.000 2.000 -62.000; 0.000 -2.038 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = Proband13_MPRAGE RegMat --------------------------- 1.000 -0.005 0.012 -2.338; -0.012 -0.026 1.000 -50.133; -0.005 -1.000 -0.026 -1.518; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8.30474, ref det = -1 Cleaning up Started at Fr 12. Sep 18:47:31 CEST 2014 Ended at Fr 12. Sep 18:48:36 CEST 2014 BBR-Run-Time-Sec 65 bbregister Done To check results, run: tkregister2 --mov /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz --reg /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2diff.bbr.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2anatorig.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Fr 12. Sep 18:48:36 CEST 2014 flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_mni.nii.gz -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anat.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2diff.bbr.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat -concat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/mni2anatorig.mat -inverse /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Fr 12. Sep 18:50:07 CEST 2014 mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 563127 values in range Counting number of voxels Found 563127 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 597612 values in range Counting number of voxels Found 597612 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 23798 values in range Counting number of voxels Found 23798 voxels in final mask mri_binarize done mri_aparc2aseg --s Proband13_MPRAGE --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/benjamin/TOSHIBA/Tinnitus/Studie1 subject Proband13_MPRAGE outvol /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.white Reading lh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/lh.pial Loading lh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.white Reading rh pial surface /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/surf/rh.pial Loading rh annotations from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/ribbon.mgz Loading filled from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1156218 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 4 clusters 0 k 920.000000 1 k 2.000000 2 k 4.000000 3 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 908.000000 1 k 2.000000 Writing output aseg to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 624225 values in range Counting number of voxels Found 624225 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 957754 values in range Counting number of voxels Found 957754 voxels in final mask mri_binarize done mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/benjamin cmdline mri_binarize --i /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz --match 16 --o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname benjamin-ThinkPad-T530 machine x86_64 user benjamin input /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 24786 values in range Counting number of voxels Found 24786 voxels in final mask mri_binarize done fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz -add /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/Brain-Stem.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/brainmask.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/mri/aparc+aseg.mgz... TR=1570.00, TE=2.63, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/notventricles.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/lowb.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi_snr.txt flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/brain_anat_orig.nii.gz -out /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fr 12. Sep 18:53:52 CEST 2014 dtifit -k /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dwi.nii.gz -m /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvecs -b /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/bvals -o /media/benjamin/TOSHIBA/Tinnitus/Studie1/Proband13_MPRAGE/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux benjamin-ThinkPad-T530 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fr 12. Sep 18:53:52 CEST 2014