Hi all,
I'm running TRACULA preprocessing in FreeSurfer 6.0 and have run into an error. It looks like it might be caused by TRACULA calling mri_convert with the input as the whole DICOM root directory, as opposed to an individual file. I'm not sure what's going wrong that leads to that happening though. I'll paste my command, error file, config file, and log file below. Thank you for any help!
Best, John
Command: trac-all -prep -c /autofs/cluster/bang/TAW_New/scripts/resources/tracula_test_config.txt
trac-all.error: ------------------------------ SUBJECT 180515_4PR00065 DATE Thu Sep 16 13:30:13 EDT 2021 USER jj1006 HOST erso.nmr.mgh.harvard.edu PROCESSOR x86_64 OS Linux 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 $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-preproc PWD /autofs/cluster/bang/TAW_New/scripts/resources CMD mri_convert /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz
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 )
trac-all.log: Thu Sep 16 13:13:39 EDT 2021 /autofs/cluster/bang/TAW_New/scripts/resources /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-all -prep -c /autofs/cluster/bang/TAW_New/scripts/resources/tracula_test_config.txt Subject 180515_4PR00065 SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c jj1006 erso.nmr.mgh.harvard.edu 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 cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked 64 kbytes maxproc 62634 maxlocks unlimited maxsignal 62634 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 16101348 5617832 4625196 263964 5858320 9883424 Swap: 16777212 4388 16772824
######################################## Program versions: $Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $ mri_convert.bin --all-info ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:39-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:39-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/16-17:13:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/16-17:13:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400
New invocation of trac-preproc
jj1006 erso.nmr.mgh.harvard.edu 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 cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked 64 kbytes maxproc 62634 maxlocks unlimited maxsignal 62634 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 16101348 5661112 4556004 263964 5884232 9840152 Swap: 16777212 4388 16772824
#------------------------------------- /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Sep 16 13:13:41 EDT 2021 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.nii.gz mri_convert.bin --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.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ 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 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.nii.gz... Saving bvals and bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.voxel_space.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.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 mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvals orientLAS /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.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.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz mri_convert.bin -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.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.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) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.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.nii.gz... INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvals /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvals eddy_correct /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.nii.gz 0 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0000 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0001 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0002 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0003 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0004 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0005 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0006 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0007 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0008 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0009 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0010 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0011 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0012 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0013 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0014 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0015 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0016 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0017 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0018 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0019 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0020 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0021 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0022 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0023 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0024 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0025 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0026 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0027 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0028 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0029 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0030 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0031 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0032 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0033 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0034 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0035 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0036 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0037 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0038 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0039 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0040 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0041 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0042 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0043 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0044 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0045 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0046 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0047 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0048 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0049 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0050 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0051 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0052 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0053 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0054 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0055 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0056 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0057 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0058 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0059 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0060 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0061 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0062 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0063 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0064 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0065 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0066 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0067 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0068 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0069 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0070 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0071 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0072 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0073 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0074 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0075 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0076 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0077 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0078 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0079 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0080 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0081 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0082 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0083 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0084 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0085 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0086 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0087 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0088 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0089 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0090 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0091 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0092 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0093 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0094 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0095 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0096 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0097 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0098 mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.norot xfmrot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.ecclog /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.norot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_eddy.nii.gz mri_convert /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz mri_convert.bin /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz corRead(): can't open file /autofs/cluster/bang/TAW_New/data/COR-.info $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/bang/TAW_New/data/... 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 Thu Sep 16 13:30:13 EDT 2021
Hi John - You're using a config file set up for the new TRACULA (in FS 7.2) and running an older version of TRACULA (from FS 6.0). You won't be able to take advantage of all the new TRACULA features with this old version. It's OK if your T1's were run through FS 6.0, you can still process your DWIs with the new version of TRACULA.
Best, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jacoby, John JJACOBY@mgh.harvard.edu Sent: Thursday, September 16, 2021 2:16 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA mri_convert error
Hi all,
I'm running TRACULA preprocessing in FreeSurfer 6.0 and have run into an error. It looks like it might be caused by TRACULA calling mri_convert with the input as the whole DICOM root directory, as opposed to an individual file. I'm not sure what's going wrong that leads to that happening though. I'll paste my command, error file, config file, and log file below. Thank you for any help!
Best, John
Command: trac-all -prep -c /autofs/cluster/bang/TAW_New/scripts/resources/tracula_test_config.txt
trac-all.error: ------------------------------ SUBJECT 180515_4PR00065 DATE Thu Sep 16 13:30:13 EDT 2021 USER jj1006 HOST erso.nmr.mgh.harvard.edu PROCESSOR x86_64 OS Linux 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 $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-preproc PWD /autofs/cluster/bang/TAW_New/scripts/resources CMD mri_convert /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz
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 )
trac-all.log: Thu Sep 16 13:13:39 EDT 2021 /autofs/cluster/bang/TAW_New/scripts/resources /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-all -prep -c /autofs/cluster/bang/TAW_New/scripts/resources/tracula_test_config.txt Subject 180515_4PR00065 SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c jj1006 erso.nmr.mgh.harvard.edu 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 cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked 64 kbytes maxproc 62634 maxlocks unlimited maxsignal 62634 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 16101348 5617832 4625196 263964 5858320 9883424 Swap: 16777212 4388 16772824
######################################## Program versions: $Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $ mri_convert.bin --all-info ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:39-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:39-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/16-17:13:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/16-17:13:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/16-17:13:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: jj1006 Machine: erso.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-310.el8.x86_64 CompilerName: GCC CompilerVersion: 40400
New invocation of trac-preproc
jj1006 erso.nmr.mgh.harvard.edu 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 cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked 64 kbytes maxproc 62634 maxlocks unlimited maxsignal 62634 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 16101348 5661112 4556004 263964 5884232 9840152 Swap: 16777212 4388 16772824
#------------------------------------- /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Sep 16 13:13:41 EDT 2021 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.nii.gz mri_convert.bin --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.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ 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 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.nii.gz... Saving bvals and bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.voxel_space.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.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 mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvals orientLAS /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.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.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz mri_convert.bin -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.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.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) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.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.nii.gz... INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvals /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvals eddy_correct /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.nii.gz 0 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0000 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0001 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0002 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0003 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0004 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0005 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0006 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0007 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0008 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0009 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0010 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0011 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0012 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0013 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0014 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0015 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0016 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0017 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0018 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0019 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0020 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0021 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0022 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0023 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0024 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0025 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0026 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0027 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0028 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0029 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0030 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0031 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0032 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0033 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0034 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0035 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0036 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0037 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0038 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0039 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0040 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0041 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0042 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0043 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0044 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0045 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0046 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0047 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0048 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0049 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0050 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0051 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0052 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0053 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0054 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0055 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0056 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0057 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0058 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0059 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0060 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0061 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0062 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0063 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0064 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0065 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0066 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0067 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0068 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0069 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0070 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0071 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0072 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0073 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0074 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0075 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0076 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0077 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0078 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0079 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0080 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0081 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0082 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0083 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0084 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0085 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0086 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0087 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0088 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0089 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0090 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0091 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0092 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0093 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0094 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0095 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0096 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0097 processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0098 mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.norot xfmrot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.ecclog /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.norot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_eddy.nii.gz mri_convert /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz mri_convert.bin /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz corRead(): can't open file /autofs/cluster/bang/TAW_New/data/COR-.info $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/bang/TAW_New/data/... 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 Thu Sep 16 13:30:13 EDT 2021
freesurfer@nmr.mgh.harvard.edu
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Jacoby, John -
Yendiki, Anastasia