I am analyzing a repeated-measures resting-state fMRI study and I would appreciate your advice regarding the structural images.

We have 22 participants who completed three experimental visits. In each visit, resting-state fMRI and a T1-weighted image were acquired both PRE and POST intervention. Therefore, each participant has six resting-state acquisitions and six corresponding T1-weighted images.

No anatomical changes are expected between these time points, since this is an acute intervention study.

For preprocessing in CONN, would you recommend using one T1-weighted image as the structural reference for all six resting-state sessions of each participant, or using the corresponding T1-weighted image for each session (session-specific structurals)?

I have seen your previous comments suggesting that a single structural image may be sufficient when no structural changes are expected across repeated measurements, but I was unsure whether the same recommendation would apply to this PRE/POST design.

Thank you very much for your help!

Best,
Liliana