Hi all,
I'm running the trac-all -prep step and it's running into an error when looking for the bvecs:
awk: fatal: cannot open file `/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs' for reading (No such file or directory)
The error is correct that dwi_orig_las.bvecs does not exist. There is however a dwi_orig_las.1.bvecs and a dwi_orig_las.2.bvecs in that same directory. Any help with this would be greatly appreciated, thank you!
Best, John
Command: trac-all -prep -c tracula_test_config.txt
Config File: setenv SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default
set dtroot = /autofs/cluster/bang/TAW_New/tracula
set dcmroot = /autofs/cluster/bang/TAW_New/data
set epifactor = 128
set echospacing = 0.69
set dob0 = 2
set interreg = 4
set subjlist = ( 180515_4PR00065 180515_4PR00065 )
set dcmlist = ( 180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 )
set pedir = ( AP PA )
Complete Log: Tue Sep 28 19:16:39 EDT 2021 /autofs/cluster/bang/TAW_New /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/trac-all -prep -jobs trac_commands.txt -c scripts/resources/tracula_test_config.txt Subject 180515_4PR00065 SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/7.2.0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/7.2.0 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b jj1006 launchpad.nmr.mgh.harvard.edu Linux launchpad.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked unlimited maxproc 127905 maxlocks unlimited maxsignal 127905 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 32778768 2017008 27346208 124188 3415552 30235716 Swap: 67108856 686920 66421936
######################################## Program versions: trac-all 7.2.0 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:39-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 FLIRT version 6.0 bbregister 7.2.0 mri_cvs_register 7.2.0 ProgramName: dmri_motion ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_motion --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_train ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_train --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_paths ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_paths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_pathstats ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_pathstats --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_mergepaths ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_mergepaths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_group ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_group --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
New invocation of trac-preproc
jj1006 compute-0-15.nmr.mgh.harvard.edu Linux compute-0-15.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 29360128 kbytes descriptors 32768 memorylocked unlimited maxproc 127909 maxlocks unlimited maxsignal 127909 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 32778856 1144720 26449592 101436 5184544 31108544 Swap: 67108860 538196 66570664
#------------------------------------- /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Sep 28 19:16:47 EDT 2021 rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz reading from /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407... Getting Series No INFO: Found 101 files in /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP INFO: Scanning for Series Number 28 Scanning Directory INFO: found 99 files in series INFO: loading series header info.
RunNo = 27 WARNING: Run 1 appears to be truncated Files Found: 99, Files Expected (lRep+1): 1 FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512220971428016067 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122239.413000 AcqTime 122131.110000 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_AP PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 27 SeriesNo 28 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 1002.7822 1063.1628 325.3363 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (140 140 92), nframes = 99, ismosaic=1 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR E11 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 3230, TR = 3230 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 /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512220971428016067 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122239.413000 AcqTime 122131.110000 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_AP PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 27 SeriesNo 28 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 98.9473 138.4093 -12.2484 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter -0.5800 11.2260 14.7653 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = 0.0130269 -0.3541 0.935117 INFO: no Siemens slice order reversal detected (good!). TR=3230.00, TE=89.20, TI=-1.00, flip angle=78.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz... Saving bvals and bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.voxel_space.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs mri_probedicom --i /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 >> /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dcminfo.dat rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz reading from /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138... Getting Series No INFO: Found 101 files in /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA INFO: Scanning for Series Number 31 Scanning Directory INFO: found 99 files in series INFO: loading series header info.
RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 99, Files Expected (lRep+1): 1 FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512275166034962234 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122828.358000 AcqTime 122712.317500 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_PA PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 1002.7822 1063.1628 325.3363 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (140 140 92), nframes = 99, ismosaic=1 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 3, short=4, float=3 Could not parse NUMARIS version string syngo MR E11 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 3230, TR = 3230 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 /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512275166034962234 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122828.358000 AcqTime 122712.317500 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_PA PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 98.9473 138.4093 -12.2484 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter -0.5800 11.2260 14.7653 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = 0.0130269 -0.3541 0.935117 INFO: no Siemens slice order reversal detected (good!). TR=3230.00, TE=89.20, TI=-1.00, flip angle=78.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz... Saving bvals and bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.voxel_space.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs mri_probedicom --i /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 >> /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dcminfo.dat rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs.tmp mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals orientLAS /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 3.375 mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz normalizing out_i_direction: (-0.999009, -0.0444233, -0.00290475) -> (-0.999009, -0.0444233, -0.00290475) normalizing out_j_direction: (-0.0425695, 0.934152, 0.354328) -> (-0.0425695, 0.934152, 0.354328) normalizing out_k_direction: (0.0130269, -0.3541, 0.935117) -> (0.0130269, -0.3541, 0.935117) reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) Reslicing using nearest writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz... INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals, copying INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs, converting to LAS rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs.tmp mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals orientLAS /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 3.375 mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz normalizing out_i_direction: (-0.999009, -0.0444233, -0.00290475) -> (-0.999009, -0.0444233, -0.00290475) normalizing out_j_direction: (-0.0425695, 0.934152, 0.354328) -> (-0.0425695, 0.934152, 0.354328) normalizing out_k_direction: (0.0130269, -0.3541, 0.935117) -> (0.0130269, -0.3541, 0.935117) reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) Reslicing using nearest writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz... INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals, copying INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs, converting to LAS mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (-0.0425695, 0.934152, 0.354328) k_ras = (0.0130269, -0.3541, 0.935117) keeping frame 0 writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz... mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (-0.0425695, 0.934152, 0.354328) k_ras = (0.0130269, -0.3541, 0.935117) keeping frame 0 writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz... mri_concat --i /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz --o /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.nii.gz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.nii.gz cp -p /usr/pubsw/packages/fsl/6.0.4//src/topup/flirtsch/b02b0.cnf /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri topup --imain=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.nii.gz --datain=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/acqp.txt --config=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b02b0.cnf --out=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/topup --iout=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_topup.nii.gz Linux compute-0-15.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Sep 28 19:53:19 EDT 2021
xfmrot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.eddy_parameters /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.bvecs awk: fatal: cannot open file `/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs' for reading (No such file or directory) awk: fatal: cannot open file `/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs' for reading (No such file or directory) ERROR: Gradient file needs to have 3 rows or 3 columns of coordinates Linux erso.nmr.mgh.harvard.edu 4.18.0-310.el8.x86_64 #1 SMP Tue Jun 8 00:24:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Sep 28 19:55:38 EDT 2021