I have a question about the exit status of 3dTrackID after an apparently successful run. 3dTrackID seemed to complete its tasks just fine, and I got my expected output, but it exited with exit status 1 rather than 0. Can anyone tell me why? When it exits with code 1, it interrupts my bash script, since I include the option 'set -o errexit'.
Here is my command and the output:
user@machine $ 3dTrackID -mode DET -dti_in dti_preprocessed/dti-afni -netrois dti_preprocessed/t2w_epi_mean-brain_mask.nii.gz -mask dti_preprocessed/t2w_epi_mean-brain_mask.nii.gz -logic OR -write_opts -do_trk_out -nifti -prefix dti_preprocessed/trackid_det
++ ROI logic type is: OR
++ Tracking mode: DET
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as dti_preprocessed/t2w_epi_mean-brain_mask.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:dti_preprocessed/t2w_epi_mean-brain_mask.nii.gz is 0.615803 degrees from plumb.
++ Number of ROIs in netw[0] = 1
++ No refset labeltable for naming things.
++ Oblique dataset:dti_preprocessed/t2w_epi_mean-brain_mask.nii.gz is 0.615803 degrees from plumb.
++
++ SEARCHING for files with prefix 'dti_preprocessed/dti-afni*'
++ Obtained 9 prefix-matching files to sort
++ SCALAR FINDINGS:
++ Oblique dataset:dti_preprocessed/dti-afni_DT.nii.gz is 0.615803 degrees from plumb.
'FA' ++ Oblique dataset:dti_preprocessed/dti-afni_FA.nii.gz is 0.615803 degrees from plumb.
'L1' ++ Oblique dataset:dti_preprocessed/dti-afni_L1.nii.gz is 0.615803 degrees from plumb.
++ Oblique dataset:dti_preprocessed/dti-afni_L2.nii.gz is 0.615803 degrees from plumb.
'L2' ++ Oblique dataset:dti_preprocessed/dti-afni_L3.nii.gz is 0.615803 degrees from plumb.
'L3' 'MD' ++ Oblique dataset:dti_preprocessed/dti-afni_MD.nii.gz is 0.615803 degrees from plumb.
++ Oblique dataset:dti_preprocessed/dti-afni_V1.nii.gz is 0.615803 degrees from plumb.
++ Oblique dataset:dti_preprocessed/dti-afni_V2.nii.gz is 0.615803 degrees from plumb.
++ Oblique dataset:dti_preprocessed/dti-afni_V3.nii.gz is 0.615803 degrees from plumb.
++ Done with scalar search, found: 6 parameters (well, including internal RD calc)
--> so will have 17 output data matrices.
++ Calculating RD
++ VECTOR FINDINGS:
++ Oblique dataset:dti_preprocessed/dti-afni_V1.nii.gz is 0.615803 degrees from plumb.
'V1' ++ Oblique dataset:dti_preprocessed/dti-afni_V2.nii.gz is 0.615803 degrees from plumb.
'V2' ++ Oblique dataset:dti_preprocessed/dti-afni_V3.nii.gz is 0.615803 degrees from plumb.
'V3'
++ With '-logic OR', the '-cut_at_rois' option will be automically turned off ('-uncut_at_rois').
++ Tracking progress count: start ...
++ Done tracking, tidying up outputs...
++ From tracking, net[0] has 149328 tracks.
++ Writing output (RPI, same as your input): dti_preprocessed/trackid_det ...
user@machine $ echo $?
1
