Analyzing sessions separately within subject


I am using singularity version 2.6.0-dist and fmriprep version 20.1.1 to preprocess functional mridata. I have three sessions per subject and would like to analyze them individually (see picture). Previous posts from 2+ years ago mention that --session-id or --session-label options were potential ways to do this but are not currently implemented. Is that still true? I tried to incorporate those flags and received an error. Is there an alternative way you recommend to analyze one session?

Thank you,

Screen Shot 2022-01-10 at 2.53.14 PM

Hi Catherine,

I would recommend updating to the most recent fmriprep build of 21.0.0 if you are just beginning processing. Old versions like that have been flagged for errors fixed in recent releases.

Now to answer your question there are a couple options:

  1. Make and pass in a --bids-filter-file (see here for an example) that specifies what session you want to process.
  2. If your storage capabilities allow it, copy just dataset_description.json and the session files you want to process to a temporary directory, and pass that into fmriprep as the BIDS root.


Hello Steven,

Thank you for your quick reply!