Tue Dec 15 16:22:35 CST 2015 /media/Data/Temple/Temple_Tracula/31313422_2998 /usr/local/freesurfer/bin/trac-all -prep -s 31313422_2998 -c 31313422_2998.dmrirc Subject 31313422_2998 SUBJECTS_DIR /media/Data/Temple/Temple_Tracula FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 11198128 5076892 4408 991940 4641408 -/+ buffers/cache: 5564780 10710240 Swap: 8208380 0 8208380 ######################################## Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:22:35-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:22:36-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:22:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:22:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:22:36-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:22:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:22:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /projects/p20394/software/freesurfer-v5.3.0 New invocation of trac-preproc root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 11236632 5038388 4408 991948 4684704 -/+ buffers/cache: 5559980 10715040 Swap: 8208380 0 8208380 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Dec 15 16:22:37 CST 2015 mri_convert /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz mri_convert /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm... crypt_gkey = *CX2cLtg3QVNM Getting Series No INFO: Found 68 files in /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom INFO: Scanning for Series Number 9 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 961.8160 942.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (122 122 55), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9900, TR = 9900 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 121.8160 102.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 1.8160 -17.3777 9.4929 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 1, correv =1, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9900.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz... crypt_gkey = *CX2cLtg3QVNM mri_probedicom --i /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm > /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dcminfo.dat Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Dec 15 16:22:54 CST 2015 New invocation of trac-all Tue Dec 15 16:28:36 CST 2015 /media/Data/Temple/Temple_Tracula/31313422_2998 /usr/local/freesurfer/bin/trac-all -prep -s 31313422_2998 -c 31313422_2998.dmrirc Subject 31313422_2998 SUBJECTS_DIR /media/Data/Temple/Temple_Tracula FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 12496268 3778752 4848 994800 5537656 -/+ buffers/cache: 5963812 10311208 Swap: 8208380 0 8208380 ######################################## Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:28:36-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:28:36-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:28:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:28:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:28:36-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:28:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:28:36-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /projects/p20394/software/freesurfer-v5.3.0 New invocation of trac-preproc root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 12496716 3778304 4848 994800 5537664 -/+ buffers/cache: 5964252 10310768 Swap: 8208380 0 8208380 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Dec 15 16:28:37 CST 2015 mri_convert /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz mri_convert /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm... crypt_gkey = *CX2cLtg3QVNM Getting Series No INFO: Found 68 files in /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom INFO: Scanning for Series Number 9 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 961.8160 942.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (122 122 55), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9900, TR = 9900 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 121.8160 102.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 1.8160 -17.3777 9.4929 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 1, correv =1, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9900.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz... crypt_gkey = *CX2cLtg3QVNM mri_probedicom --i /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm > /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dcminfo.dat New invocation of trac-all Tue Dec 15 16:36:56 CST 2015 /media/Data/Temple/Temple_Tracula/31313422_2998 /usr/local/freesurfer/bin/trac-all -prep -s 31313422_2998 -c 31313422_2998.dmrirc Subject 31313422_2998 SUBJECTS_DIR /media/Data/Temple/Temple_Tracula FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 13146580 3128440 4848 996052 5720788 -/+ buffers/cache: 6429740 9845280 Swap: 8208380 0 8208380 ######################################## Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:36:56-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:36:56-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:36:56-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:36:56-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:36:56-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:36:56-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:36:56-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /projects/p20394/software/freesurfer-v5.3.0 New invocation of trac-preproc root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 13147136 3127884 4848 996052 5720788 -/+ buffers/cache: 6430296 9844724 Swap: 8208380 0 8208380 New invocation of trac-all Tue Dec 15 16:43:50 CST 2015 /media/Data/Temple/Temple_Tracula/31313422_2998 /usr/local/freesurfer/bin/trac-all -prep -s 31313422_2998 -c 31313422_2998.dmrirc Subject 31313422_2998 SUBJECTS_DIR /media/Data/Temple/Temple_Tracula FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 13755580 2519440 5104 997112 5919484 -/+ buffers/cache: 6838984 9436036 Swap: 8208380 0 8208380 ######################################## Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:43:50-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:43:50-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:43:51-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:43:51-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:43:51-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:43:51-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:43:51-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /projects/p20394/software/freesurfer-v5.3.0 New invocation of trac-preproc root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 13755248 2519772 5104 997112 5919488 -/+ buffers/cache: 6838648 9436372 Swap: 8208380 0 8208380 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Dec 15 16:43:52 CST 2015 mri_convert /media/Data/Temple/Temple_Tracula//31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz mri_convert /media/Data/Temple/Temple_Tracula//31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /media/Data/Temple/Temple_Tracula//31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm... crypt_gkey = *CX2cLtg3QVNM Getting Series No INFO: Found 68 files in /media/Data/Temple/Temple_Tracula//31313422_2998/dti_dicom INFO: Scanning for Series Number 9 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/Data/Temple/Temple_Tracula//31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 961.8160 942.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (122 122 55), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9900, TR = 9900 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /media/Data/Temple/Temple_Tracula//31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 121.8160 102.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 1.8160 -17.3777 9.4929 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 1, correv =1, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9900.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz... crypt_gkey = *CX2cLtg3QVNM mri_probedicom --i /media/Data/Temple/Temple_Tracula//31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm > /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dcminfo.dat New invocation of trac-all Tue Dec 15 16:48:24 CST 2015 /media/Data/Temple/Temple_Tracula/31313422_2998 /usr/local/freesurfer/bin/trac-all -prep -s 31313422_2998 -c 31313422_2998.dmrirc Subject 31313422_2998 SUBJECTS_DIR /media/Data/Temple/Temple_Tracula FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 14461520 1813500 5312 999152 6132268 -/+ buffers/cache: 7330100 8944920 Swap: 8208380 0 8208380 ######################################## Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:24-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:24-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:24-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:24-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:24-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:24-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:24-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /projects/p20394/software/freesurfer-v5.3.0 New invocation of trac-preproc root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 14465300 1809720 5312 999152 6132428 -/+ buffers/cache: 7333720 8941300 Swap: 8208380 0 8208380 New invocation of trac-all Tue Dec 15 16:48:43 CST 2015 /media/Data/Temple/Temple_Tracula/31313422_2998 /usr/local/freesurfer/bin/trac-all -prep -s 31313422_2998 -c 31313422_2998.dmrirc Subject 31313422_2998 SUBJECTS_DIR /media/Data/Temple/Temple_Tracula FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 14727784 1547236 5312 1230068 6132284 -/+ buffers/cache: 7365432 8909588 Swap: 8208380 0 8208380 ######################################## Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:43-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:43-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:43-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:43-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:43-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:43-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/15-22:48:43-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /projects/p20394/software/freesurfer-v5.3.0 New invocation of trac-preproc root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63462 total used free shared buffers cached Mem: 16275020 14773876 1501144 5312 1266736 6132604 -/+ buffers/cache: 7374536 8900484 Swap: 8208380 0 8208380 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Dec 15 16:48:45 CST 2015 mri_convert /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz mri_convert /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm... crypt_gkey = *CX2cLtg3QVNM Getting Series No INFO: Found 68 files in /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom INFO: Scanning for Series Number 9 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 961.8160 942.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (122 122 55), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9900, TR = 9900 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName 31313422_2998 Date and time StudyDate 20140521 StudyTime 105357.765000 SeriesTime 115737.203000 AcqTime 115503.847500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI_64 Directions PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 9900 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 976 NImageCols 976 NFrames 65 SliceArraylSize 55 IsMosaic 1 ImgPos 121.8160 102.6223 -59.2571 VolRes 1.9672 1.9672 2.5000 VolDim 122 122 55 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 1.8160 -17.3777 9.4929 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 1, correv =1, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=9900.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dwi_orig.nii.gz... crypt_gkey = *CX2cLtg3QVNM mri_probedicom --i /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR.Temple.9.1.20140521.105357.1f9ykdm.dcm > /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dcminfo.dat