Processing Future fMRI Data Using Results from Earlier fMRIprep Preprocessing

Hello everyone!

I was hoping to run a question by you really quick about if a certain feature exists with fMRIprep. For one of our studies, a study participant will receive their baseline scan, then be scanned again 7-10 days later after a treatment has been applied during that time. Then, the subject comes back in for a three-month follow up scan to see if there were any noticeable lasting affects of the treatment in brain connectivity and function. If I wait until a subject receives all three scans, the process is easy. Their data is set up as “ses-1,” “ses-2,” and “ses-3.” For the normalization (and correct me if I am incorrect here), the T1w images from scans 2 and three are aligned with the T1w from scan 1, and the T1w from scan 1 is what is normalized during fMRIprep.

If I wanted to process subjects after their second scan to save time (since we won’t get their next scan for 3 months), is there a way to use the outputs from the fMRIprep processing for scans 1 and 2 to then process scan 3 when we get it? Or would I have to just completely redo all three scans once the third scan is performed? Would there be a way to use the normalized T1w created from the preprocessing of scans 1 and 2 as the normalization target for the native space T1w from scan 3? Or something along those lines?

After thinking about the issue, one possible alternative would be to simply use the T1w from scan 1 as the T1w for the third scan once we perform the scan, but if there is already a built-in longitudinal feature for fMRIprep, that would be preferable.

Thank you for reading.