Hi,
I successfully ran 3dTrackID PROB with a test subject and also using a for loop with two subjects at a time. I now wish to run it for all my subjects (n = 330) using a parallel nohup command. However, I received the error below (here is one example, which is repeated several times for all subjects). Any ideas why? thanks!

Command I ran:
find SPN01* -type f | nohup parallel 'dtipath="/home/eji/projects/spins/preproc/fsl/subjects/w0" && cd {} && cd afni && 3dTrackID -mode PROB -uncert DWUncert+orig. -netrois $dtipath/{}/mri/parc5002dwi.nii.gz -mask $dtipath/{}/MASK.nii.gz -prefix 3dTrackID_prob -dti_in 3dDWItoDT_ -alg_Thresh_FA 0.2 -alg_Nmonte 1000 -alg_Nseed_Vox 5 -alg_Thresh_Frac 0.1 -nifti -dump_rois AFNI -no_indipair_out -overwrite' ::: * &


Output:

++ Tracking mode: PROB
++ Number of ROIs in netw[0] = 318
++ No refset labeltable for naming things.
++ SEARCHING for vector files with prefix '3dDWItoDT_*':
FINDING: 'V1' 'V2' 'V3'
++ SEARCHING for scalar files with prefix '3dDWItoDT_*':
FINDING: not:'DT' 'FA' 'L1' not:'L2' not:'L3' 'MD' 'RD'
++ Done with scalar search, found: 4 parameters
--> so will have 15 output data matrices.
++ Effective Monte iterations: 5000. Fraction threshold set: 0.10000
--> Ntrack voxel threshold: 500.
++ Tracking progress count: start ...

Fatal Signal 11 (SIGSEGV) received
Bottom of Debug Stack
** AFNI version = AFNI_20.1.06 Compile date = May 4 2020
** [[Precompiled binary linux_ubuntu_16_64: May 4 2020]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/eji/.afni.crashlog

++ Tracking mode: PROB
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /home/eji/projects/spins/preproc/fsl/subjects/w0/SPN01_MRC_0009_01/mri/parc5002dwi.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/home/eji/projects/spins/preproc/fsl/subjects/w0/SPN01_MRC_0009_01/mri/parc5002dwi.nii.gz is 14.799997 degrees from plumb.
++ Number of ROIs in netw[0] = 318
++ No refset labeltable for naming things.
++ Oblique dataset:/home/eji/projects/spins/preproc/fsl/subjects/w0/SPN01_MRC_0009_01/MASK.nii.gz is 14.799997 degrees from plumb.
++ SEARCHING for vector files with prefix '3dDWItoDT_*':
FINDING: 'V1' 'V2' 'V3'
++ SEARCHING for scalar files with prefix '3dDWItoDT_*':
FINDING: not:'DT' 'FA' 'L1' not:'L2' not:'L3' 'MD' 'RD'
++ Done with scalar search, found: 4 parameters
--> so will have 15 output data matrices.
** FATAL ERROR: Input datasets do not match in number of voxels!
'-netrois' volume has 1081344 vox,
'-uncert' volume has 1750656 vox,
'-inset' volume has 1750656 vox,
** Program compile date = May 4 2020



Edited 1 time(s). Last edit at 10/12/2020 08:12AM by eji.