Running fMRIPrep on a single run

Hi all,

I’m trying to run fMRIPrep on a single run (apparently a few of my nii.gz’s are corrupted and unreadable).
My task files (BIDS) look like:

Now, I know I have the –anat-derivatives options which will spare me from reprocessing the anat, and the –task-id flag that will spare me the rest and leave me with the task only. However, given I have a single rest and 6 task (mental) scans - is there a way to ask also for only one of the runs (it’s only one of the runs that is unreadable)?


P.S. - I see there was once a -r flag, but gone…

You can pass in a —bids-filter-file JSON file ( for example) that specifies which run you want to process. If you are on a HPC and can spare the temporary storage usage you can also just copy the necessary files you want to process to a single-subject single-run BIDS directory in scratch space and delete it when processing is done.