Fri Feb 3 11:18:35 CET 2012 /Applications/freesurfer/subjects/TRACULA/DTI /Applications/freesurfer/bin/trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc Subject 3001_JoEd_8502 SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 benjamingarzon 130-229-40-185.cns.ki.se Darwin 130-229-40-185.cns.ki.se 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 2560 memorylocked unlimited maxproc 266 PhysMem: 755M wired, 1496M active, 189M inactive, 2439M used, 1651M free. ######################################## Program versions: $Id: trac-all,v 1.22.2.6 2011/05/24 06:49:09 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/02/03-10:18:37-GMT BuildTimeStamp: May 25 2011 22:32:58 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: benjamingarzon Machine: 130-229-40-185.cns.ki.se Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000 FLIRT version 5.5 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ $Id: mri_cvs_register,v 1.15.2.8 2011/05/23 12:37:47 lzollei Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/02/03-10:18:37-GMT BuildTimeStamp: May 25 2011 22:32:58 CVS: User: benjamingarzon Machine: 130-229-40-185.cns.ki.se Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/02/03-10:18:37-GMT BuildTimeStamp: May 25 2011 22:32:58 CVS: User: benjamingarzon Machine: 130-229-40-185.cns.ki.se Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/02/03-10:18:37-GMT BuildTimeStamp: May 25 2011 22:32:58 CVS: User: benjamingarzon Machine: 130-229-40-185.cns.ki.se Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/02/03-10:18:37-GMT BuildTimeStamp: May 25 2011 22:32:58 CVS: User: benjamingarzon Machine: 130-229-40-185.cns.ki.se Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000 New invocation of trac-preproc benjamingarzon 130-229-40-185.cns.ki.se Darwin 130-229-40-185.cns.ki.se 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 2560 memorylocked unlimited maxproc 266 PhysMem: 756M wired, 1498M active, 218M inactive, 2471M used, 1623M free. #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Feb 3 11:18:38 CET 2012 mri_convert /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/orig/00000001.dcm /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig.nii.gz mri_convert /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/orig/00000001.dcm /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/orig/00000001.dcm... Starting DICOMRead2() dcmfile = /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/orig/00000001.dcm dcmdir = /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/orig Ref Series No = 5 Found 3905 files, checking for dicoms Found 3900 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2.9 Vs: 0 0 1 Second Sorting Counting frames nframes = 65 nslices = 60 ndcmfiles = 3900 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=8000.00, TE=82.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig.nii.gz... mri_probedicom --i /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/orig/00000001.dcm > /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dcminfo.dat flip4fsl /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig.nii.gz /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2.54883 fslswapdim /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig.nii.gz x -y z /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig_flip.nii.gz mv -f /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig_flip.mghdti.bvecs /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/bvecs mv: rename /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/dwi_orig_flip.mghdti.bvecs to /Applications/freesurfer/subjects/TRACULA/DTI//3001_JoEd_8502/dmri/bvecs: No such file or directory Darwin 130-229-40-185.cns.ki.se 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Feb 3 11:23:40 CET 2012