Frmiprep: how to incorporate pre-run freesurfer?

fmriprep

#1

I’m sorry if this has already been asked somewhere.

How/can I run fmriprep without having to rerun freesurfer if I already have surfaces for my participants? I have two use cases for this:

  1. re-running the functional processing with different parameters
  2. working with freesurfer outputs from the HCPPipelines…

It sounds (from some other threads) like this is possible, but we are having trouble figuring it out the command-line args for it from the docs.

Thanks,
Erin


#2

When you run fmriprep, you should specify an output directory.

If you place your precomputed FreeSurfer results at that point, they will automatically be taken in by fmriprep.

In practice: if you intend to point your outputs to /some/output/folder, then store the FreeSurfer directory under that folder (/some/output/folder/freesurfer). The tree should look then like:

/some/output/folder/
  freesurfer/
      fsaverage{,5,6}/
          mri/
          surf/
          ...
      sub-<subject_label>/
          mri/
          surf/
          ...
      ...

Finally, you call fmriprep like fmriprep /path/to/bids_root /some/output/folder --participant_label <subject_label>

Cheers,
Oscar


#3

But it looks it still rerun the freesurfer even under the /some/output/folder/freesurfer folder.
How should we avoid reruning freesurfer?


#4

Can you share your full command, as well as the output that indicates re-running FreeSurfer?