Tracula prepocessing error awk: fatal: cannot open file dmri/dwi_orig_las.1.bvals - Freesurfer

7 Feb 2022


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Hi all,
I was trying to run trac-all preprocessing and it seems there is a problem with eddy_openmp. The program is unable to find the dwi_orig_las.1.bvals file which makes that the index.txt is empty.
see the terminal output:
trac-all -prep -c tracula_config
INFO: SUBJECTS_DIR is /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI
INFO: Diffusion root is /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI
Actual FREESURFER_HOME /share/opt/freesurfer-7.2.0
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
trac-preproc -c /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/dmrirc.local -log /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/trac-all.log -cmd /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/trac-all.cmd
#-------------------------------------
/opt/freesurfer-7.2.0/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Mon Feb  7 15:56:50 CET 2022
rm -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs
mri_convert --bvec-voxel /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz
mri_convert --bvec-voxel /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz 
reading from /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz...
TR=900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1e-16, 0)
j_ras = (1e-16, 0.92521, 0.379456)
k_ras = (-3.79456e-17, -0.379456, 0.92521)
writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz...
rm -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs.tmp
mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs
mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals
orientLAS /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -7.86266
mri_convert -oni 116 -onj 116 -onk 72 -oid -1 1e-16 0 -ojd 1e-16 0.92521 0.379456 -okd -3.79456e-17 -0.379456 0.92521 -oc 2.02404 20.3466 -11.1417 -rt nearest /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz
mri_convert -oni 116 -onj 116 -onk 72 -oid -1 1e-16 0 -ojd 1e-16 0.92521 0.379456 -okd -3.79456e-17 -0.379456 0.92521 -oc 2.02404 20.3466 -11.1417 -rt nearest /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz 
normalizing out_j_direction: (1e-16, 0.92521, 0.379456) -> (1e-16, 0.92521, 0.379456)
normalizing out_k_direction: (-3.79456e-17, -0.379456, 0.92521) -> (-3.79456e-17, -0.379456, 0.92521)
reading from /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz...
TR=900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1e-16, 0)
j_ras = (1e-16, 0.92521, 0.379456)
k_ras = (-3.79456e-17, -0.379456, 0.92521)
Reslicing using nearest 
writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz...
INFO: found /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals, copying
INFO: found /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs, converting to LAS
mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz
mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvecs /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvecs
mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvals /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvals
mri_convert --frame 0 /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz
mri_convert --frame 0 /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz 
reading from /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz...
TR=900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1e-16, 0)
j_ras = (1e-16, 0.92521, 0.379456)
k_ras = (-3.79456e-17, -0.379456, 0.92521)
keeping frame 0
writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz...
bet /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las_brain.nii.gz -m -f 0.3
awk: fatal: cannot open file `/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory)
eddy_openmp --imain=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz --mask=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvecs --bvals=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvals --acqp=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/acqp.txt --index=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/index.txt --data_is_shelled --out=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi
EddyInputError:  Error when attempting to read --index file
Terminating program
Linux ipsnode-7-2.local 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Feb  7 15:57:40 CET 2022
I checked the dmri directory and there is no dwi_orig_las.1.bvals. However there is a file named `dwi_orig_las.bvals`. Could the issue be that the file is not properly named?
Thanks in advance
Vicente Ferrer
Predoctoral Researcher BCBL
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