I have a dataset with two timepoints, pre and post neurosurgery. I have two specific needs:
- I would like one freesurfer datapoint per timepoint, in order to do repeated-measures analysis of cortical thickness for both timepoints on non-operated brain tissue.
- I would like fmriprep to exclusively use the pre-surgical timepoint for it’s internal freesurfer processing.
In this situation, would it make the most sense to run freesurfer outside of fmriprep for (1) and run fmriprep with the
--longitudinal flag for (2)? I am worried that if fmriprep does any sort of anatomical averaging between pre- and post-surgical timepoints, the quality of the segmentations it will use will be compromised.