Hi,

I have been trying different ways to troubleshooting this error without success. I am pasting here the whole error when I try to run  "trac-all -prep -c"  in the Dev version:

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon
INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b
Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b
Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864
trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.cmd ; trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.cmd ;
#-------------------------------------
/usr/local/freesurfer/dev/bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Apr 27 09:37:59 EDT 2020
mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz
mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz
reading from /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010...
Getting Series No
INFO: Found 5211 files in /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715
INFO: Scanning for Series Number 102
Scanning Directory
INFO: found 140 files in series
INFO: loading series header info.

RunNo = 101
INFO: sorting.
sdfiSameSlicePos() eps = 0.000001

WARNING: file /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 does not contain a Siemens ASCII header
has this file been anonymized?
Proceeding as best as I can ...

INFO: (256 256 140), nframes = 1, ismosaic=0
sdfi->UseSliceScaleFactor 0
INFO: rescale not needed
datatype = 4, short=4, float=3
PE Dir ROW ROW
FileName /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010
Identification
NumarisVer        syngo MR E11
ScannerModel      Prisma_fit
PatientName       3LT050_s1_170715
Date and time
StudyDate         20170715
StudyTime         092536.870000
SeriesTime        100956.320000
AcqTime           093429.902500
Acquisition parameters
PulseSeq          tfl_me3d4_16ns
Protocol          T1
PhEncDir          ROW
EchoNo            1
FlipAngle         7
EchoTime          1.69
InversionTime     1100
RepetitionTime    2530
PhEncFOV          0
ReadoutFOV        0
Image information
RunNo             101
SeriesNo          102
ImageNo           139
NImageRows        256
NImageCols        256
NFrames           1
SliceArraylSize   0
IsMosaic          0
ImgPos             54.1349  92.6115 176.0819
VolRes              1.0000   1.0000   1.0000
VolDim            256      256      140
Vc                  0.0934  -0.9338  -0.3453
Vr                  0.0226   0.3487  -0.9370
Vs                  0.4326   0.3520  -0.8301
VolCenter          99.2585  42.3521 -46.1506
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
INFO: no Siemens slice order reversal detected (good!).
TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00
i_ras = (0.0933703, -0.933839, -0.345291)
j_ras = (0.0225973, 0.348705, -0.93696)
k_ras = (0.432568, 0.35197, -0.830061)
writing to /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz...
mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat
ERROR: Must specify input table of gradient vectors
Linux deqi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020

#-------------------------------------
/usr/local/freesurfer/dev/bin/trac-preproc
#-------------------------------------
#@# Inter-subject registration (base template) Mon Apr 27 09:39:14 EDT 2020
cp /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms
cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory
cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory
Linux deqi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020

[deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat
[deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat
[deqi:Scripts] (nmr-dev-env) autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms
autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat: Command not found.
[deqi:Scripts] (nmr-dev-env) cp autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms
cp: cannot stat \u2018autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory
cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory


Thanks for the help, Gabriela
From: Figueiro Longo, Maria Gabriela
Sent: Friday, April 24, 2020 10:47 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Tracula error: ERROR: Must specify input table of gradient vectors
 
Hello Dear Freesurfer Developers,

I am attempting to run Tracula in the last to subject of my study (I had processed all the other subjects using the same script without problems). However, when I try to run the scrip bellow, I am having the error:

" ERROR: Must specify input table of gradient vectors "

 I am reviewed the associated DICOM images and couldn't find any problem with the images. I reviewed a couple emails in the list, but couldn't find a clear reason for keeping having this error.

I am using the Freesurfer Dev version.

I really appreciate any help.

Thank you, Gabriela



# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output

# Subject IDs (one per time point per subject)
#
set subjlist = ( 3LT050_s1_170715 )

# Longitudinal base template subject IDs (one for each time point above)
#
set baselist = ( 3LT050 )

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#
# set runlist = (1 2 5 6)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified (see below)
#
set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data
set dcmlist = ( 3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.20170715092715598296003 )



Gabriela Longo, MD, MSc.


Emergency Radiology Clinical Fellow, Emergency Radiology Division

Massachusetts General Hospital (MGH)

mfigueirolongo@mgh.harvard.edu

Phone: +1 857 214 0568