Hi AFNI gurus:

Was hoping for a little advice.

For a new study we scan on two consecutive days (each a different condition). Each day gets the same task-based fMRI, resting-state scans, and a MEMPRAGE scan. One of the days also gets a Diffusion weighted scan. My goal is to compare these metrics between days/conditions within-subject, but keep as many of the imaging modalities linked to each other as possible.

Right now I use Freesurfer+SUMA to reconstruct the MEMPRAGE and use it as a base for functional analyses (both task and resting), and for diffusion-scans using FAT)CAT to link it all together. Thought given that the Diffusion image is only on Day 2, I've started questioning which T1/MEMPRAGE scan to use.

Is it better to use each day's own scan as an anatomical base (i suppose theoretically closer in alignment to the functionals) but each day's data would be out of alignment with the other day's, or pick the best scan of either day and use it for "everything." The benefit of the latter approach would clearly be that all data for both days has an identical registration base and therefore easily related to one-another.

Anyone have similar pipelines for their data?

Thanks in advance for the insight!!!
Jared