Running fMRIPrep on a Single Session Without Overwriting Existing Data

[swwalsh1]

Hi everyone,

As part of our study, we’ve been using fMRIPrep (v20.2.6) to process pre-treatment scans for our participants. We’ve now started collecting post-treatment scans and would like to run fMRIPrep on just the post-treatment session without affecting the existing pre-treatment data.

Is it possible to process only the post-treatment session without overwriting the current fMRIPrep outputs? Specifically, I’m concerned about the sub-SUBJID.html QC report—will it get overwritten by the new run, or does fMRIPrep automatically merge the QC reports for multiple sessions into a single file?

Thanks in advance for your help!

[Steven]

Hi @swwalsh1,

Yes, with BIDS filter files. FAQ - Frequently Asked Questions — fmriprep version documentation

@swwalsh1

Specifically, I’m concerned about the sub-SUBJID.html QC report—will it get overwritten by the new run, or does fMRIPrep automatically merge the QC reports for multiple sessions into a single file?

I don’t remember what the behavior is like in the version you’re using. At worst case, in your script you can just rename them before running fmriprep.

Best,
Steven

[effigies]

If you reuse output directories, you can probably expect some rough edges. It would be safest to use fresh output directories, and merge the results manually.