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Hi Freesurfer team!
I am having an issue with the -jobs flag for trac-all -bedp in freesurfer/7.3.0. I ran trac-all -prep with the -jobs flag with no issue, and submitted the commands as jobs on my cluster without error. However, when I try to create the commands for -bedp with the -jobs flag, I get the following error message:
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /projects/dsnlab/shared/tag/nonbids_data/dMRI/tracula/sub-001w01/dmri/nodif_brain_mask.nii.gz pre./projects/dsnlab/shared/tag/TAG_scripts/dMRI/tracula/trac-all_bedp: No such file or directory.
The directory in the last line does not exist, so perhaps it's not surprising that I am getting an error with that. However, if I submit the trac-all -bedp command on my cluster directly (without the -jobs flag), it runs without error. I am also able to get the desired output with the -jobs flag for trac-all -path and trac-all -stat (both after running -bedp), so I am not sure what is causing the error using the -jobs flag with trac-all -bedp.
Does anyone have any insight as to how I can address this? Ultimately, I'll be running trac-all on a longitudinal data set with many subjects, so I plan to run everything in parallel.
I've attached my config file (just one test subject) below. Thanks in advance for the help!
Best, Chris