Dear. Freesurfer experts.

Hi. How are you?

I have dataset where a single subject was scanned twice on different days.

I ran recon-all in logitudinal stream (cross, base, long). The recon-all -base gave me the within-subject template and the recon-all -long gave me the directory in the format of tp1id.long.templateID. By doing so, I get different time point's norm.mgz (under tp1id.long.templateID directory and tp2id.long.templateID etc) aligned in the same voxel space.

As a next step, I'd like to register the functional scans to the anatomical scans via preproc-sess (or mc-sess, spmregister-sess etc). I guess, the anatomical can that I should use is norm.mgz under tp1id.long.templateID directory and tp2id.long.templateID etc. (?)

To register the functional scans to the newly created anatomical image obtained from recon-all -long process (norm.mgz under tp1id.long.templateID directory and tp2id.long.templateID etc), I think I should specify this newly created norm.mgz in the command line... but couldn't figure it out yet.

The preproc-sess command that I used in the cross-sectional process is as below: preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_decode -per-run -force -fwhm 0

What should I do to make registration process target a specific anatomical image?

Please give me any advice!

Thank you so much for your help!

Best, Ji Won