I have seen a few posts here about using multiple sessions with a single anatomy, which works fine when you run them all at once. I have also seen references to using the “–bids-filter-file” to restrict processing to a single session. I can’t seem to find the proper way to run a single session from a multi-session BOLD, where it uses the anatomical outputs from a previous fmriprep run. My setup has:
bids/derivatives/freesurfer/sub-01/mri etc...
bids/sub-01/ses-01/anat/*T1w.{nii.gz}
bids/sub-01/ses-01/func/*bold.{nii.gz}
bids/sub-01/ses-02/func/*bold.{nii.gz}
outputs/sub-01/ses-01/anat/<lots of files>
outputs/sub-01/ses-01/func/<lots of files>
I want to run on only ses-02, using the files from outputs/sub-01/ses-01/anat/<lots of files> so I don’t have to rerun any of those steps (or have them interfere if I run ses-03 in parallel). I’ve tried adding --bids-filter-file with a file containing:
{ "bold": {"datatype": "func", "session": "02", "suffix": "bold" } }
But it still tries to re-run the anat steps. I have also tried copying outputs/sub-01/ses-01/anat/<lots of files> to bids/derivatives/sub-01/ses-01/anat/ and adding --derivatives bids/derivatives but it still reruns those steps.
In the notes for --bids-filter-file, it seems this is one of the cases that is designed for (like the MyConnectome case). But I can’t figure out how to make it work. Any help would be appreciated!
Edit: Want to add that my ultimate goal is to process 50+ bold session for this subject in parallel, so avoiding file collisions is a priority.