I’ve been noticing that when I run the default fmriprep on subjects that have more than 1 T1 (so 2 sessions), that derivatives/fmriprep seems to look fine. However when I look under derivatives/freesurfer/sub-hc0xx/mri/orig/ it only has 001.mgz. Shouldn’t there be a 002.mgz file in there as well, since there are 2 T1 files? I looked on freesurfer’s usage doc, and noticed that if you have more than 1 T1 file, you can enter “recon-all -i file1 -i file2”… does fmriprep account for this by default, or is there a way to specify this? I am using version 1.4.1 singularity (older since, we gotta stick with the same version for our study) if that helps.
Otherwise I think I would have to run the freesurfer separately from the fmriprep call and link the freesurfer output to fmriprep?? Any clarification/help would be appreciated,