Fre Aug 16 16:45:57 CEST 2013 /data/physics/florian/data_nft /usr/local/freesurfer/bin/trac-all -prep -c /data/physics/florian/dmrirc_6dir Subject 1020000485074_20080319 SUBJECTS_DIR /data/physics/florian/fs FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 neurophysics pu02neu003 Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 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 192270 maxlocks unlimited maxsignal 192270 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 24679544 23928248 751296 0 881424 6387948 -/+ buffers/cache: 16658876 8020668 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: 2013/08/16-14:45:57-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: neurophysics Machine: pu02neu003 Platform: Linux PlatformVersion: 3.5.0-34-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $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: 2013/08/16-14:45:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: neurophysics Machine: pu02neu003 Platform: Linux PlatformVersion: 3.5.0-34-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/16-14:45:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: neurophysics Machine: pu02neu003 Platform: Linux PlatformVersion: 3.5.0-34-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/16-14:45:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: neurophysics Machine: pu02neu003 Platform: Linux PlatformVersion: 3.5.0-34-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/16-14:45:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: neurophysics Machine: pu02neu003 Platform: Linux PlatformVersion: 3.5.0-34-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc neurophysics pu02neu003 Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 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 192270 maxlocks unlimited maxsignal 192270 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 24679544 23930892 748652 0 881424 6387948 -/+ buffers/cache: 16661520 8018024 Swap: 0 0 0 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fre Aug 16 16:45:58 CEST 2013 mri_convert /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.nii.gz mri_convert /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM... Getting Series No INFO: Found 58 files in /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2 INFO: Scanning for Series Number 9 Scanning Directory INFO: found 56 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 1 appears to be truncated Files Found: 56, Files Expected (lRep+1): 8 FileName /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName AAAAAA Date and time StudyDate 20080319 StudyTime 093334.578000 SeriesTime 100726.484000 AcqTime 100548.362500 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_2b_6d_grpa2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 81 InversionTime -1 RepetitionTime 4900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 896 NImageCols 896 NFrames 56 SliceArraylSize 40 IsMosaic 1 ImgPos 843.6656 853.4301 -62.8985 VolRes 1.8750 1.8750 3.0000 VolDim 128 128 40 Vc -0.9996 -0.0017 -0.0295 Vr 0.0000 -0.9983 0.0581 Vs -0.0295 0.0581 0.9979 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 40), nframes = 56, ismosaic=1 Could not parse NUMARIS version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 4900, TR = 4900 ms PE Dir COL COL 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 /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName AAAAAA Date and time StudyDate 20080319 StudyTime 093334.578000 SeriesTime 100726.484000 AcqTime 100548.362500 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_2b_6d_grpa2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 81 InversionTime -1 RepetitionTime 4900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 896 NImageCols 896 NFrames 56 SliceArraylSize 40 IsMosaic 1 ImgPos 123.9795 133.4112 -42.2885 VolRes 1.8750 1.8750 3.0000 VolDim 128 128 40 Vc -0.9996 -0.0017 -0.0295 Vr 0.0000 -0.9983 0.0581 Vs -0.0295 0.0581 0.9979 VolCenter 2.2603 16.8925 21.0191 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0.029525 0.0580748 0.997876 INFO: no Siemens slice order reversal detected (good!). TR=4900.00, TE=81.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (3.5909e-08, -0.998311, 0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.nii.gz... mri_probedicom --i /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM > /data/physics/florian/data_nft/1020000485074_20080319/dmri/dcminfo.dat cp /data/physics/florian/data_nft/1020000485074_20080319/data/1020000485074_20080319_diff_oriented.bvec /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs cp /data/physics/florian/data_nft/1020000485074_20080319/data/1020000485074_20080319_diff_oriented.bval /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10.5469 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.nii.gz x -y z /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz INFO: found /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig_flip.mghdti.bvecs /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvecs mv -f /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig_flip.mghdti.bvals /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvals eddy_correct /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz 0 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0000 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0001 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0002 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0003 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0004 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0005 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0006 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0007 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0008 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0009 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0010 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0011 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0012 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0013 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0014 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0015 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0016 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0017 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0018 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0019 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0020 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0021 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0022 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0023 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0024 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0025 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0026 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0027 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0028 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0029 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0030 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0031 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0032 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0033 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0034 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0035 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0036 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0037 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0038 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0039 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0040 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0041 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0042 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0043 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0044 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0045 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0046 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0047 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0048 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0049 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0050 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0051 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0052 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0053 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0054 processing /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_tmp0055 mv -f /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvecs /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvecs.norot xfmrot /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.ecclog /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvecs.norot /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvecs ln -sf /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/data.nii.gz mri_convert --frame 0 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 0 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame0.nii.gz... mri_convert --frame 7 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame7.nii.gz mri_convert --frame 7 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame7.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 7 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame7.nii.gz... mri_convert --frame 14 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame14.nii.gz mri_convert --frame 14 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame14.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 14 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame14.nii.gz... mri_convert --frame 21 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame21.nii.gz mri_convert --frame 21 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame21.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 21 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame21.nii.gz... mri_convert --frame 28 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame28.nii.gz mri_convert --frame 28 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame28.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 28 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame28.nii.gz... mri_convert --frame 35 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame35.nii.gz mri_convert --frame 35 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame35.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 35 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame35.nii.gz... mri_convert --frame 42 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame42.nii.gz mri_convert --frame 42 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame42.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 42 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame42.nii.gz... mri_convert --frame 49 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame49.nii.gz mri_convert --frame 49 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame49.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 49 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame49.nii.gz... mri_concat --i /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame0.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame7.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame14.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame21.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame28.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame35.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame42.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_frame49.nii.gz --mean --o /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz ninputs = 8 Checking inputs nframestot = 8 Allocing output Done allocing nframes = 8 Computing mean across frames Writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz bet /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb_brain_mask.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff #------------------------------------- #@# Intra-subject registration Fre Aug 16 16:59:21 CEST 2013 mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brain.mgz /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_orig.nii.gz mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brain.mgz /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/fs/1020000485074_20080319/mri/brain.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.07122e-08, -4.65661e-10) j_ras = (-9.31323e-10, 5.82077e-11, -1) k_ras = (1.45138e-08, 1, -5.82077e-11) writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_orig.nii.gz... flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_orig.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_orig.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat.nii.gz tkregister2 --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_orig.nii.gz --targ /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2anat.mat --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2anatorig.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat.nii.gz movable volume /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_orig.nii.gz reg file /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2anatorig.mat -inverse /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2anat.mat Log file is /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.log Fre Aug 16 16:59:24 CEST 2013 setenv SUBJECTS_DIR /data/physics/florian/fs cd /data/physics/florian/data_nft /usr/local/freesurfer/bin/bbregister --s 1020000485074_20080319 --init-fsl --dti --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --fslmat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii mri_convert /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii... fslregister --s 1020000485074_20080319 --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister --dof 6 --fsvol brainmask.mgz Log file is /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat.fslregister.log Fre Aug 16 16:59:30 CEST 2013 --s 1020000485074_20080319 --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ pu02neu003 Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /data/physics/florian/data_nft mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/refvol.fslregister.nii mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.07122e-08, -4.65661e-10) j_ras = (-9.31323e-10, 5.82077e-11, -1) k_ras = (1.45138e-08, 1, -5.82077e-11) writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/refvol.fslregister.nii... -------------------------------------- /data/physics/florian/data_nft mri_convert /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/movvol.fslregister.nii --frame 0 mri_convert /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999564, -0.00171544, -0.0294751) j_ras = (-3.5909e-08, 0.998311, -0.0581001) k_ras = (-0.029525, 0.0580748, 0.997876) keeping frame 0 writing to /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/movvol.fslregister.nii... Mov determinant is -10.5469 /data/physics/florian/data_nft tkregister2_cmdl --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/movvol.fslregister.nii --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/reg0.30970.dat --regheader --fslregout /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat.fsl.mat0 --s 1020000485074_20080319 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/movvol.fslregister.nii reg file /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/reg0.30970.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 /data/physics/florian/fs/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.875 0.000 0.000 120.000; 0.000 0.000 3.000 -60.000; 0.000 -1.875 0.000 120.000; 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 0.002 0.029 1.940; -0.030 0.058 0.998 -46.564; 0.000 -0.998 0.058 -6.142; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.002 0.029 1.940; -0.030 0.058 0.998 -46.564; 0.000 -0.998 0.058 -6.142; 0.000 0.000 0.000 1.000; Determinant 1 subject = 1020000485074_20080319 RegMat --------------------------- 1.000 0.002 0.029 1.940; -0.030 0.058 0.998 -46.564; 0.000 -0.998 0.058 -6.142; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -10.5469, ref det = -1 Fre Aug 16 16:59:39 CEST 2013 /data/physics/florian/data_nft flirt.fsl -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/refvol.fslregister.nii -in /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat.fsl.mat0 Fre Aug 16 16:59:51 CEST 2013 /data/physics/florian/data_nft flirt.fsl -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/refvol.fslregister.nii -in /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat.fsl.mat -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s 1020000485074_20080319 --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat --fslreg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.998 -0.062 0.004 15.806; 0.009 0.091 -0.996 132.589; 0.062 0.994 0.091 -6.436; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii reg file /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/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 /data/physics/florian/fs/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii Tmov: -------------------- -1.875 0.000 0.000 120.000; 0.000 0.000 3.000 -60.000; 0.000 -1.875 0.000 120.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -10.5469, ref det = -1 ---- Input registration matrix (computed) -------- 0.998 -0.062 0.009 -0.256; -0.004 0.091 0.996 -42.794; -0.062 -0.994 0.091 -6.192; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 -0.062 0.009 -0.256; -0.004 0.091 0.996 -42.794; -0.062 -0.994 0.091 -6.192; 0.000 0.000 0.000 1.000; Determinant 1 subject = 1020000485074_20080319 RegMat --------------------------- 0.998 -0.062 0.009 -0.256; -0.004 0.091 0.996 -42.794; -0.062 -0.994 0.091 -6.192; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: _ (standard_in) 1: syntax error Started at Fre Aug 16 16:59:30 CEST 2013 Ended at Fre Aug 16 17:00:32 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat --surf orig mri_segreg --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --init-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat --out-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/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 /data/physics/florian/fs cd /data/physics/florian/data_nft mri_segreg --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --init-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat --out-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/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 pu02neu003 machine x86_64 user neurophysics movvol /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii regfile /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.init.dat subject 1020000485074_20080319 dof 6 outregfile /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/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 1377401486 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 -0.062 0.009 -0.256; -0.004 0.091 0.996 -42.794; -0.062 -0.994 0.091 -6.192; 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 1.016056 1 -25.0 -25.0 25.0 1.056254 2 -25.0 25.0 -25.0 1.031998 3 -25.0 25.0 25.0 0.978608 4 25.0 -25.0 -25.0 1.023124 5 25.0 -25.0 25.0 0.991830 6 25.0 25.0 -25.0 1.025478 7 25.0 25.0 25.0 1.021861 REL: 8 0.352095 8.145208 1.018151 rel = 0.345818 Initial costs ---------------- Number of surface hits 2851 WM Intensity 230.3028 +/- 52.2290 Ctx Intensity 285.4129 +/- 77.4484 Pct Contrast 19.7018 +/- 25.2371 Cost 0.3521 RelCost 0.3458 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0101 1.0101 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9933 0.9933 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9469 0.9469 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9307 0.9307 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9214 0.9214 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8861 0.8861 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8641 0.8641 0.0 36 -4.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.8106 0.8106 0.0 117 -4.0000 0.0000 0.0000 0.0000 -4.0000 -4.0000 0.8102 0.8102 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7949 0.7949 0.0 135 -4.0000 0.0000 4.0000 -4.0000 -4.0000 -4.0000 0.7932 0.7932 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7038 0.7038 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6770 0.6770 0.0 361 0.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.6388 0.6388 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5524 0.5524 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3521 0.3521 0.0 Brute Force -------------------------- Min cost was 0.352095 Number of iterations 729 Search time 3.961000 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 8 0.026 0.000 0.000 0.000 0.000 0.000 0.3517391285 10 0.062 0.000 0.000 0.000 0.000 0.000 0.3514171795 13 0.061 0.000 0.000 0.000 0.000 0.000 0.3514158609 17 0.060 0.000 0.000 0.000 0.000 0.000 0.3514157290 21 0.060 -1.618 0.000 0.000 0.000 0.000 0.3437549856 22 0.060 -0.861 0.000 0.000 0.000 0.000 0.3098969405 27 0.060 -0.736 0.000 0.000 0.000 0.000 0.3086304333 29 0.060 -0.773 0.000 0.000 0.000 0.000 0.3085731376 31 0.060 -0.757 0.000 0.000 0.000 0.000 0.3084895104 33 0.060 -0.753 0.000 0.000 0.000 0.000 0.3084886592 35 0.060 -0.754 0.000 0.000 0.000 0.000 0.3084878444 38 0.060 -0.754 1.000 0.000 0.000 0.000 0.2909187916 42 0.060 -0.754 0.618 0.000 0.000 0.000 0.2891661964 43 0.060 -0.754 0.724 0.000 0.000 0.000 0.2888843421 45 0.060 -0.754 0.736 0.000 0.000 0.000 0.2888593270 47 0.060 -0.754 0.775 0.000 0.000 0.000 0.2887694663 48 0.060 -0.754 0.799 0.000 0.000 0.000 0.2886919698 54 0.060 -0.754 0.799 -1.618 0.000 0.000 0.2567588000 55 0.060 -0.754 0.799 -1.138 0.000 0.000 0.2537133667 58 0.060 -0.754 0.799 -1.321 0.000 0.000 0.2507861058 60 0.060 -0.754 0.799 -1.286 0.000 0.000 0.2505768888 62 0.060 -0.754 0.799 -1.294 0.000 0.000 0.2505564550 70 0.060 -0.754 0.799 -1.294 -0.618 0.000 0.2170934457 72 0.060 -0.754 0.799 -1.294 -0.791 0.000 0.2146627176 74 0.060 -0.754 0.799 -1.294 -0.782 0.000 0.2146366979 76 0.060 -0.754 0.799 -1.294 -0.758 0.000 0.2145553436 77 0.060 -0.754 0.799 -1.294 -0.743 0.000 0.2145514596 78 0.060 -0.754 0.799 -1.294 -0.749 0.000 0.2145455729 85 0.060 -0.754 0.799 -1.294 -0.749 -0.618 0.1984095648 87 0.060 -0.754 0.799 -1.294 -0.749 -0.566 0.1979268609 90 0.060 -0.754 0.799 -1.294 -0.749 -0.576 0.1978693603 92 0.060 -0.754 0.799 -1.294 -0.749 -0.579 0.1978626748 102 0.110 -0.754 0.799 -1.294 -0.749 -0.579 0.1962734742 103 0.178 -0.754 0.799 -1.294 -0.749 -0.579 0.1961273772 105 0.148 -0.754 0.799 -1.294 -0.749 -0.579 0.1958774299 116 0.148 -0.850 0.799 -1.294 -0.749 -0.579 0.1941877832 117 0.148 -0.862 0.799 -1.294 -0.749 -0.579 0.1941598499 120 0.148 -0.863 0.799 -1.294 -0.749 -0.579 0.1941597745 127 0.148 -0.863 0.919 -1.294 -0.749 -0.579 0.1932016811 128 0.148 -0.863 0.910 -1.294 -0.749 -0.579 0.1931750502 129 0.148 -0.863 0.899 -1.294 -0.749 -0.579 0.1931730176 131 0.148 -0.863 0.904 -1.294 -0.749 -0.579 0.1931678091 143 0.148 -0.863 0.904 -1.312 -0.749 -0.579 0.1931539615 144 0.148 -0.863 0.904 -1.304 -0.749 -0.579 0.1931407002 146 0.148 -0.863 0.904 -1.303 -0.749 -0.579 0.1931405523 155 0.148 -0.863 0.904 -1.303 -0.772 -0.579 0.1928932790 158 0.148 -0.863 0.904 -1.303 -0.789 -0.579 0.1928597573 159 0.148 -0.863 0.904 -1.303 -0.788 -0.579 0.1928593585 160 0.148 -0.863 0.904 -1.303 -0.787 -0.579 0.1928590006 163 0.148 -0.863 0.904 -1.303 -0.786 -0.579 0.1928587911 172 0.148 -0.863 0.904 -1.303 -0.786 -0.622 0.1925105807 173 0.148 -0.863 0.904 -1.303 -0.786 -0.641 0.1925052286 174 0.148 -0.863 0.904 -1.303 -0.786 -0.633 0.1924958439 186 0.152 -0.863 0.904 -1.303 -0.786 -0.633 0.1924950815 187 0.151 -0.863 0.904 -1.303 -0.786 -0.633 0.1924947492 199 0.151 -0.845 0.904 -1.303 -0.786 -0.633 0.1923555701 211 0.151 -0.845 0.901 -1.303 -0.786 -0.633 0.1923545073 224 0.151 -0.845 0.901 -1.306 -0.786 -0.633 0.1923525921 233 0.151 -0.845 0.901 -1.306 -0.787 -0.633 0.1923480346 234 0.151 -0.845 0.901 -1.306 -0.814 -0.633 0.1923413105 236 0.151 -0.845 0.901 -1.306 -0.802 -0.633 0.1923240081 237 0.151 -0.845 0.901 -1.306 -0.803 -0.633 0.1923233972 249 0.151 -0.845 0.901 -1.306 -0.803 -0.641 0.1923193185 250 0.151 -0.845 0.901 -1.306 -0.803 -0.638 0.1923179454 262 0.146 -0.845 0.901 -1.306 -0.803 -0.638 0.1923079026 263 0.144 -0.845 0.901 -1.306 -0.803 -0.638 0.1923071840 276 0.144 -0.842 0.901 -1.306 -0.803 -0.638 0.1923011322 277 0.144 -0.841 0.901 -1.306 -0.803 -0.638 0.1923006558 287 0.144 -0.841 0.906 -1.306 -0.803 -0.638 0.1922918301 289 0.144 -0.841 0.909 -1.306 -0.803 -0.638 0.1922900609 290 0.144 -0.841 0.908 -1.306 -0.803 -0.638 0.1922899120 301 0.144 -0.841 0.908 -1.312 -0.803 -0.638 0.1922827654 302 0.144 -0.841 0.908 -1.311 -0.803 -0.638 0.1922820482 312 0.144 -0.841 0.908 -1.311 -0.804 -0.638 0.1922818466 325 0.144 -0.841 0.908 -1.311 -0.804 -0.639 0.1922816453 336 0.143 -0.841 0.908 -1.311 -0.804 -0.639 0.1922806019 337 0.141 -0.841 0.908 -1.311 -0.804 -0.639 0.1922798580 360 0.141 -0.841 0.907 -1.311 -0.804 -0.639 0.1922797260 371 0.141 -0.841 0.907 -1.312 -0.804 -0.639 0.1922796376 381 0.141 -0.841 0.907 -1.312 -0.803 -0.639 0.1922795310 394 0.141 -0.841 0.907 -1.312 -0.803 -0.638 0.1922793603 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.008197 1 -25.0 -25.0 25.0 1.040647 2 -25.0 25.0 -25.0 1.013724 3 -25.0 25.0 25.0 0.971294 4 25.0 -25.0 -25.0 1.014794 5 25.0 -25.0 25.0 0.989281 6 25.0 25.0 -25.0 1.001577 7 25.0 25.0 25.0 1.039681 REL: 8 0.192279 8.079195 1.009899 rel = 0.190395 Number of iterations 4 Min cost was 0.192279 Number of FunctionCalls 396 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.278000 sec Parameters at optimum (transmm) 0.14101 -0.84064 0.90749 Parameters at optimum (rotdeg) -1.31205 -0.80316 -0.63848 Final costs ---------------- Number of surface hits 2851 WM Intensity 221.3414 +/- 50.2306 Ctx Intensity 283.7556 +/- 68.7123 Pct Contrast 23.7100 +/- 21.9804 Cost 0.1923 RelCost 0.3458 Reg at min cost was 0.999 -0.047 0.019 -0.520; -0.016 0.069 0.998 -43.760; -0.048 -0.997 0.068 -4.306; 0.000 0.000 0.000 1.000; Writing optimal reg to /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/bbr.pass1.dat, type = 14 Original Reg 0.998 -0.062 0.009 -0.256; -0.004 0.091 0.996 -42.794; -0.062 -0.994 0.091 -6.192; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.001 -0.015 -0.010 0.264; 0.013 0.022 -0.002 0.966; -0.014 0.003 0.023 -1.886; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.249894 Computing change in rh position Surface RMS Diff (mm) 1.588729 3.420876 mri_segreg done mri_segreg --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --init-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/bbr.pass1.dat --out-reg /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/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 /data/physics/florian/fs cd /data/physics/florian/data_nft mri_segreg --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii --init-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/bbr.pass1.dat --out-reg /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname pu02neu003 machine x86_64 user neurophysics movvol /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/template.nii regfile /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/tmp.bbregister.30934/bbr.pass1.dat subject 1020000485074_20080319 dof 6 outregfile /data/physics/florian/data_nft/1020000485074_20080319/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 1376771835 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.047 0.019 -0.520; -0.016 0.069 0.998 -43.760; -0.048 -0.997 0.068 -4.306; 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 0.989194 1 -25.0 -25.0 25.0 1.022331 2 -25.0 25.0 -25.0 1.004167 3 -25.0 25.0 25.0 1.004099 4 25.0 -25.0 -25.0 1.022683 5 25.0 -25.0 25.0 1.013470 6 25.0 25.0 -25.0 1.032700 7 25.0 25.0 25.0 1.029271 REL: 8 0.189212 8.117914 1.014739 rel = 0.186464 Initial costs ---------------- Number of surface hits 282618 WM Intensity 221.7666 +/- 53.6626 Ctx Intensity 286.1719 +/- 70.9834 Pct Contrast 24.3679 +/- 22.5488 Cost 0.1892 RelCost 0.1865 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1996 0.1996 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1994 0.1994 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1994 0.1994 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1976 0.1976 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1964 0.1964 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1963 0.1963 0.0 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1961 0.1961 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.1959 0.1959 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.1956 0.1956 0.0 20 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.1948 0.1948 0.0 35 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.1944 0.1944 0.0 71 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.1000 0.1935 0.1935 0.0 361 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.1934 0.1934 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1923 0.1923 0.0 Brute Force -------------------------- Min cost was 0.192279 Number of iterations 729 Search time 4.073000 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 -0.069 0.000 0.000 0.000 0.000 0.000 0.1890082835 17 -0.069 -0.199 0.000 0.000 0.000 0.000 0.1870176707 18 -0.069 -0.192 0.000 0.000 0.000 0.000 0.1870080001 19 -0.069 -0.184 0.000 0.000 0.000 0.000 0.1870063682 20 -0.069 -0.186 0.000 0.000 0.000 0.000 0.1870058285 29 -0.069 -0.186 0.129 0.000 0.000 0.000 0.1860621580 30 -0.069 -0.186 0.128 0.000 0.000 0.000 0.1860596670 31 -0.069 -0.186 0.118 0.000 0.000 0.000 0.1860547369 33 -0.069 -0.186 0.119 0.000 0.000 0.000 0.1860546142 41 -0.069 -0.186 0.119 0.070 0.000 0.000 0.1860523839 42 -0.069 -0.186 0.119 0.035 0.000 0.000 0.1859824018 51 -0.069 -0.186 0.119 0.035 0.189 0.000 0.1837879222 53 -0.069 -0.186 0.119 0.035 0.177 0.000 0.1837780918 55 -0.069 -0.186 0.119 0.035 0.176 0.000 0.1837779804 63 -0.069 -0.186 0.119 0.035 0.176 -0.068 0.1837022363 65 -0.069 -0.186 0.119 0.035 0.176 -0.067 0.1837019786 66 -0.069 -0.186 0.119 0.035 0.176 -0.063 0.1837012229 70 -0.069 -0.186 0.119 0.035 0.176 -0.062 0.1837011201 78 -0.118 -0.186 0.119 0.035 0.176 -0.062 0.1834568021 79 -0.132 -0.186 0.119 0.035 0.176 -0.062 0.1834356938 81 -0.136 -0.186 0.119 0.035 0.176 -0.062 0.1834349396 90 -0.136 -0.168 0.119 0.035 0.176 -0.062 0.1834116931 92 -0.136 -0.169 0.119 0.035 0.176 -0.062 0.1834116102 101 -0.136 -0.169 0.072 0.035 0.176 -0.062 0.1833532905 103 -0.136 -0.169 0.085 0.035 0.176 -0.062 0.1833456969 104 -0.136 -0.169 0.084 0.035 0.176 -0.062 0.1833456100 112 -0.136 -0.169 0.084 0.101 0.176 -0.062 0.1833279433 113 -0.136 -0.169 0.084 0.072 0.176 -0.062 0.1832859421 114 -0.136 -0.169 0.084 0.071 0.176 -0.062 0.1832855420 115 -0.136 -0.169 0.084 0.065 0.176 -0.062 0.1832851617 117 -0.136 -0.169 0.084 0.067 0.176 -0.062 0.1832848932 125 -0.136 -0.169 0.084 0.067 0.205 -0.062 0.1832307504 126 -0.136 -0.169 0.084 0.067 0.207 -0.062 0.1832302186 127 -0.136 -0.169 0.084 0.067 0.208 -0.062 0.1832302112 137 -0.136 -0.169 0.084 0.067 0.208 -0.058 0.1832298440 153 -0.147 -0.169 0.084 0.067 0.208 -0.058 0.1832234933 154 -0.145 -0.169 0.084 0.067 0.208 -0.058 0.1832232199 155 -0.144 -0.169 0.084 0.067 0.208 -0.058 0.1832231658 163 -0.144 -0.165 0.084 0.067 0.208 -0.058 0.1832197255 164 -0.144 -0.161 0.084 0.067 0.208 -0.058 0.1832197206 166 -0.144 -0.162 0.084 0.067 0.208 -0.058 0.1832195502 167 -0.144 -0.163 0.084 0.067 0.208 -0.058 0.1832194546 176 -0.144 -0.163 0.082 0.067 0.208 -0.058 0.1832191918 185 -0.144 -0.163 0.082 0.082 0.208 -0.058 0.1832080525 186 -0.144 -0.163 0.082 0.083 0.208 -0.058 0.1832078853 187 -0.144 -0.163 0.082 0.085 0.208 -0.058 0.1832078376 197 -0.144 -0.163 0.082 0.085 0.213 -0.058 0.1832069926 199 -0.144 -0.163 0.082 0.085 0.212 -0.058 0.1832069913 208 -0.144 -0.163 0.082 0.085 0.212 -0.072 0.1832055322 209 -0.144 -0.163 0.082 0.085 0.212 -0.067 0.1832050130 220 -0.151 -0.163 0.082 0.085 0.212 -0.067 0.1832038174 221 -0.149 -0.163 0.082 0.085 0.212 -0.067 0.1832035188 230 -0.149 -0.160 0.082 0.085 0.212 -0.067 0.1831993064 231 -0.149 -0.149 0.082 0.085 0.212 -0.067 0.1831961775 233 -0.149 -0.152 0.082 0.085 0.212 -0.067 0.1831954893 244 -0.149 -0.152 0.078 0.085 0.212 -0.067 0.1831946724 254 -0.149 -0.152 0.078 0.086 0.212 -0.067 0.1831941678 255 -0.149 -0.152 0.078 0.090 0.212 -0.067 0.1831931876 276 -0.149 -0.152 0.078 0.090 0.213 -0.072 0.1831923553 277 -0.149 -0.152 0.078 0.090 0.213 -0.071 0.1831922945 285 -0.151 -0.148 0.077 0.092 0.213 -0.073 0.1831908587 286 -0.151 -0.148 0.076 0.092 0.213 -0.073 0.1831907604 287 -0.151 -0.147 0.076 0.092 0.213 -0.074 0.1831907577 288 -0.151 -0.147 0.076 0.092 0.213 -0.073 0.1831907558 289 -0.151 -0.147 0.076 0.092 0.213 -0.073 0.1831907131 290 -0.151 -0.147 0.076 0.092 0.213 -0.073 0.1831906667 293 -0.151 -0.147 0.076 0.092 0.213 -0.073 0.1831906385 302 -0.155 -0.147 0.076 0.092 0.213 -0.073 0.1831897565 303 -0.156 -0.147 0.076 0.092 0.213 -0.073 0.1831897540 312 -0.156 -0.147 0.076 0.092 0.213 -0.083 0.1831893758 313 -0.156 -0.147 0.076 0.092 0.213 -0.079 0.1831888529 325 -0.156 -0.147 0.077 0.092 0.213 -0.079 0.1831888103 343 -0.156 -0.147 0.077 0.092 0.212 -0.079 0.1831887119 351 -0.156 -0.146 0.077 0.093 0.212 -0.079 0.1831884896 352 -0.156 -0.146 0.077 0.093 0.212 -0.079 0.1831884663 355 -0.156 -0.146 0.077 0.093 0.212 -0.079 0.1831884634 369 -0.157 -0.146 0.077 0.093 0.212 -0.079 0.1831884330 379 -0.157 -0.146 0.077 0.093 0.212 -0.080 0.1831884133 408 -0.157 -0.146 0.077 0.093 0.211 -0.080 0.1831883556 417 -0.157 -0.146 0.077 0.093 0.211 -0.080 0.1831883204 481 -0.157 -0.146 0.077 0.093 0.211 -0.080 0.1831883183 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 0.988170 1 -25.0 -25.0 25.0 1.022487 2 -25.0 25.0 -25.0 1.006132 3 -25.0 25.0 25.0 1.002057 4 25.0 -25.0 -25.0 1.022293 5 25.0 -25.0 25.0 1.013936 6 25.0 25.0 -25.0 1.033168 7 25.0 25.0 25.0 1.028554 REL: 8 0.183188 8.116796 1.014600 rel = 0.180552 Number of iterations 6 Min cost was 0.183188 Number of FunctionCalls 488 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 71.332000 sec Parameters at optimum (transmm) -0.15732 -0.14580 0.07683 Parameters at optimum (rotdeg) 0.09270 0.21076 -0.08045 Final costs ---------------- Number of surface hits 282618 WM Intensity 221.2824 +/- 54.0193 Ctx Intensity 285.6875 +/- 69.6304 Pct Contrast 24.5458 +/- 22.3053 Cost 0.1832 RelCost 0.1865 Reg at min cost was 0.998 -0.051 0.021 -0.755; -0.017 0.070 0.997 -43.898; -0.052 -0.996 0.069 -4.298; 0.000 0.000 0.000 1.000; Writing optimal reg to /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 0.999 -0.047 0.019 -0.520; -0.016 0.069 0.998 -43.760; -0.048 -0.997 0.068 -4.306; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.004 -0.002 0.235; 0.001 -0.002 0.000 0.138; 0.004 -0.000 -0.002 -0.008; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.305245 Computing change in rh position Surface RMS Diff (mm) 0.298596 0.478660 mri_segreg done tkregister2_cmdl --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz reg file /data/physics/florian/data_nft/1020000485074_20080319/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 -------- 0.998 -0.051 0.021 -0.755; -0.017 0.070 0.997 -43.898; -0.052 -0.996 0.069 -4.298; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /data/physics/florian/fs/1020000485074_20080319/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 /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz Tmov: -------------------- -1.875 0.000 0.000 120.000; 0.000 0.000 3.000 -60.000; 0.000 -1.875 0.000 120.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.998 -0.051 0.021 -0.755; -0.017 0.070 0.997 -43.898; -0.052 -0.996 0.069 -4.298; 0.000 0.000 0.000 1.000; Determinant 1 subject = 1020000485074_20080319 RegMat --------------------------- 0.998 -0.051 0.021 -0.755; -0.017 0.070 0.997 -43.898; -0.052 -0.996 0.069 -4.298; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -10.5469, ref det = -1 Cleaning up Started at Fre Aug 16 16:59:24 CEST 2013 Ended at Fre Aug 16 17:02:32 CEST 2013 BBR-Run-Time-Sec 188 bbregister Done To check results, run: tkregister2 --mov /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.mat -inverse /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -concat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.mat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2anatorig.mat convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2anat.bbr.mat -inverse /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Fre Aug 16 17:02:32 CEST 2013 flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_mni.nii.gz -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/mni2anat.mat -inverse /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2mni.bbr.mat -concat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat -inverse /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2mni.mat -concat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2anat.mat convert_xfm -omat /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/mni2anatorig.mat -inverse /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Fre Aug 16 17:05:46 CEST 2013 mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/physics/florian/data_nft cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname pu02neu003 machine x86_64 user neurophysics input /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /data/physics/florian/data_nft/1020000485074_20080319/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 582742 values in range Counting number of voxels Found 582742 voxels in final mask mri_binarize done mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/physics/florian/data_nft cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname pu02neu003 machine x86_64 user neurophysics input /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /data/physics/florian/data_nft/1020000485074_20080319/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 613368 values in range Counting number of voxels Found 613368 voxels in final mask mri_binarize done mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/physics/florian/data_nft cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname pu02neu003 machine x86_64 user neurophysics input /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 7114 values in range Counting number of voxels Found 7114 voxels in final mask mri_binarize done mri_aparc2aseg --s 1020000485074_20080319 --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /data/physics/florian/fs subject 1020000485074_20080319 outvol /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/fs/1020000485074_20080319/surf/lh.white Reading lh pial surface /data/physics/florian/fs/1020000485074_20080319/surf/lh.pial Loading lh annotations from /data/physics/florian/fs/1020000485074_20080319/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 /data/physics/florian/fs/1020000485074_20080319/surf/rh.white Reading rh pial surface /data/physics/florian/fs/1020000485074_20080319/surf/rh.pial Loading rh annotations from /data/physics/florian/fs/1020000485074_20080319/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 /data/physics/florian/fs/1020000485074_20080319/mri/ribbon.mgz Loading filled from /data/physics/florian/fs/1020000485074_20080319/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 /data/physics/florian/fs/1020000485074_20080319/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 = 1041158 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 1 clusters 0 k 1202.000000 Fixing Parahip RH WM Found 4 clusters 0 k 1.000000 1 k 1.000000 2 k 1190.000000 3 k 1.000000 Writing output aseg to /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/physics/florian/data_nft cmdline mri_binarize --i /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz sysname Linux hostname pu02neu003 machine x86_64 user neurophysics input /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 483708 values in range Counting number of voxels Found 483708 voxels in final mask mri_binarize done mri_binarize --i /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/physics/florian/data_nft cmdline mri_binarize --i /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname pu02neu003 machine x86_64 user neurophysics input /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 808514 values in range Counting number of voxels Found 808514 voxels in final mask mri_binarize done mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 16 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/physics/florian/data_nft cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 16 --o /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname pu02neu003 machine x86_64 user neurophysics input /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 22404 values in range Counting number of voxels Found 22404 voxels in final mask mri_binarize done fslmaths /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz -add /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.07122e-08, -4.65661e-10) j_ras = (-9.31323e-10, 5.82077e-11, -1) k_ras = (1.45138e-08, 1, -5.82077e-11) writing to /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz -mul /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz /data/physics/florian/data_nft/1020000485074_20080319/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 /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.07122e-08, -4.65661e-10) j_ras = (-9.31323e-10, 5.82077e-11, -1) k_ras = (1.45138e-08, 1, -5.82077e-11) writing to /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/White-Matter.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/notventricles.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/notventricles.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/notventricles.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/notventricles.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/cortex.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz -k /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi_snr.txt flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/lowb_brain_mask.nii.gz -ref /data/physics/florian/data_nft/1020000485074_20080319/dmri/brain_anat_orig.nii.gz -out /data/physics/florian/data_nft/1020000485074_20080319/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data/physics/florian/data_nft/1020000485074_20080319/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fre Aug 16 17:20:24 CEST 2013 dtifit -k /data/physics/florian/data_nft/1020000485074_20080319/dmri/dwi.nii.gz -m /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvecs -b /data/physics/florian/data_nft/1020000485074_20080319/dmri/bvals -o /data/physics/florian/data_nft/1020000485074_20080319/dmri/dtifit Error: bvecs and bvals don't have the same number of entries #------------------------------------- #@# Priors Fre Aug 16 17:20:25 CEST 2013 /usr/local/freesurfer/bin/dmri_train --outdir /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.1020000485074_20080319.29347.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz --fa /data/physics/florian/data_nft/1020000485074_20080319/dmri/dtifit_FA.nii.gz --cptdir /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat --ncpts 5 --trunc cwd /data/physics/florian/data_nft cmdline /usr/local/freesurfer/bin/dmri_train --outdir /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.1020000485074_20080319.29347.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz --fa /data/physics/florian/data_nft/1020000485074_20080319/dmri/dtifit_FA.nii.gz --cptdir /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff --reg /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat --ncpts 5 --trunc sysname Linux hostname pu02neu003 machine x86_64 user neurophysics Output directory: /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni Output directory in test subject's space: /data/physics/florian/data_nft/1020000485074_20080319/dlabel/diff Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.1020000485074_20080319.29347.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz FA map for output subject: /data/physics/florian/data_nft/1020000485074_20080319/dmri/dtifit_FA.nii.gz Affine registration from atlas to base for output subject: /data/physics/florian/data_nft/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat Number of control points for initial spline: 5 Exclude previously chosen center streamlines: 0 Use truncated streamlines: 1 Loading brain mask of output subject from /data/physics/florian/data_nft/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz Loading FA map of output subject from /data/physics/florian/data_nft/1020000485074_20080319/dmri/dtifit_FA.nii.gz niiRead(): error opening file /data/physics/florian/data_nft/1020000485074_20080319/dmri/dtifit_FA.nii.gz ERROR: Could not read /data/physics/florian/data_nft/1020000485074_20080319/dmri/dtifit_FA.nii.gz #------------------------------------- trac-preproc finished without error at Fre Aug 16 17:20:26 CEST 2013