fMRIprep and freesurfer: would like one freesurfer reconstruction per timepoint

I have a dataset with two timepoints, pre and post neurosurgery. I have two specific needs:

  1. 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.
  2. 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.


Yes, and to make organization easier for the second question, each time point should be a separate folder. So you would have something like derivatives/freesurfer-pre/sub-01 And something similar for post.

No. The —longitudinal stream creates an unbiased template from all images, whereas the default is to align to first image. If you only want fmriprep to use the pre time point, you can pass in the pre folder we specified above to the fs-subject-dir Fmriprep argument.


1 Like