Hi John - Did the topup command near the end of the logfile work? For example was this file created:
/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_topup.nii.gz

Anastasia.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jacoby, John <JJACOBY@mgh.harvard.edu>
Sent: Wednesday, September 29, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA Locating Bvecs Error
 
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