Thu Feb 4 12:22:43 CET 2016 /dat/Hirnreifung/Auswertung/Skripte /usr/local/freesurfer/bin/trac-all -prep -c dmrirc Subject 3001LT SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 parzerpeter wkjp01 Linux wkjp01 3.16.0-60-generic #80~14.04.1-Ubuntu SMP Wed Jan 20 13:37:48 UTC 2016 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 31450 maxlocks unlimited maxsignal 31450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8081052 7946996 134056 314180 610604 5162520 -/+ buffers/cache: 2173872 5907180 Swap: 7811068 131548 7679520 ######################################## 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: 2016/02/04-11:22:43-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: parzerpeter Machine: wkjp01 Platform: Linux PlatformVersion: 3.16.0-60-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: 2016/02/04-11:22:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: parzerpeter Machine: wkjp01 Platform: Linux PlatformVersion: 3.16.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/02/04-11:22:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: parzerpeter Machine: wkjp01 Platform: Linux PlatformVersion: 3.16.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/02/04-11:22:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: parzerpeter Machine: wkjp01 Platform: Linux PlatformVersion: 3.16.0-60-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/02/04-11:22:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: parzerpeter Machine: wkjp01 Platform: Linux PlatformVersion: 3.16.0-60-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc parzerpeter wkjp01 Linux wkjp01 3.16.0-60-generic #80~14.04.1-Ubuntu SMP Wed Jan 20 13:37:48 UTC 2016 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 31450 maxlocks unlimited maxsignal 31450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8081052 7862916 218136 314236 610608 5078484 -/+ buffers/cache: 2173824 5907228 Swap: 7811068 131548 7679520 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Feb 4 12:22:43 CET 2016 mri_convert /dat/Hirnreifung/Daten/DICOM/3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig.nii.gz mri_convert /dat/Hirnreifung/Daten/DICOM/3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /dat/Hirnreifung/Daten/DICOM/3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm... Getting Series No INFO: Found 6452 files in /dat/Hirnreifung/Daten/DICOM/3001LT/d_Diff_ax_64dir_1av_b0_1000_3000 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 6450 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: ( 96 96 50), nframes = 129, ismosaic=0 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 /dat/Hirnreifung/Daten/DICOM/3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0050.dcm Identification NumarisVer syngo MR B20P ScannerModel Biograph_mMR PatientName 3001LT Date and time StudyDate 20140602 StudyTime 152153.597000 SeriesTime 153922.519000 AcqTime 153907.327500 Acquisition parameters PulseSeq *ep_b0 Protocol d_Diff_ax_64dir_1av_b0_1000_3000 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 112 InversionTime -1 RepetitionTime 12100 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 1 SeriesNo 2 ImageNo 50 NImageRows 96 NImageCols 96 NFrames 129 SliceArraylSize 50 IsMosaic 0 ImgPos 119.1690 137.1875 -7.9510 VolRes 2.5000 2.5000 2.5000 VolDim 96 96 50 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter -0.8310 17.1875 54.5490 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=12100.00, TE=112.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig.nii.gz... mri_probedicom --i /dat/Hirnreifung/Daten/DICOM/3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm > /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dcminfo.dat flip4fsl /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig.nii.gz /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 15.625 fslswapdim /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig.nii.gz x -y z /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig_flip.nii.gz mv -f /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig_flip.mghdti.bvecs /dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/bvecs mv: cannot stat '/dat/Hirnreifung/Auswertung/freesurfer/3001LT/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux wkjp01 3.16.0-60-generic #80~14.04.1-Ubuntu SMP Wed Jan 20 13:37:48 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Feb 4 12:36:53 CET 2016