Integrate FastSurfer with fMRIPrep

Software Support
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Dear all,

I would like to use FastSurfer (instead of FreeSurfer) for my fMRI analysis with fMRIprep and XCP-D. I have run FastSurfer v2.3.0 and am planning to use fMRIprep 24.1.0 and XCP-D 0.11.0. According to fMRIprep v24.0.0 release notes:

New features include separation of HTML reports by session for subjects with many BOLD runs, a new --fs-no-resume option to improve interoperability with less typical FreeSurfer directories, such as those generated by longitudinal FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow the recommendations of recent versions of BIDS.

I have two questions:

  1. Which arguments should I use for fMRIprep call? For now, I provide FastSurfer output directory as --fs-subjects-dir and include --fs-no-resume; however, the boilerplate indicates that “FreeSurfer reconstruction: Run by fMRIPrep”. Is the boilerplate wrong or do I need to add aditional arguments to the fMRIprep call?
  2. Does the same usage fits to the latest fMRIprep versions, i.e., 25.x?

Best,
Amir

2

Hi @AmirHussein,

Boilerplate is wrong. Those are correct flags.

Yes.

Best,
Steven