Can fMRIPrep use session specific freesurfer output to preprocess multiple sessions per subject?

I posted in another thread but I did not clearly state my initial issue, and the thread got off track. I am posting again with hopes of some clarification regarding using pre-run Freesurfer outputs from multiple sessions in fMRIPrep.

The Study:

  • We are conducting a multiple session study (two timepoints), and expecting GM change and functional change between each subject’s sessions.

The Data:

  • We have pre-run Freesurfer for each subject’s session, processed cross-sectionally (i.e. not using Freesurfer longitudinal pipeline).

The Desired behavior:

  • We would like to use our pre-run and QC’d Freesurfer output at each subject’s session to separately process fMRI data at each subject’s related session.
  • That is, we want each session’s fMRIPrep functional pre-processing to use the corresponding pre-run QC’d Freesurfer output.
  • For example,
    • Subject 1: FS Session 1 for fMRIprep Session 1; FS Session 2 for fMRIPres Session 2.
    • Subject 2: FS Session 1 for fMRIprep Session 1; FS Session 2 for fMRIPres Session 2.

The problem:

  • When placing pre-run Freesurfer outputs in /out/freesurfer/sub-1 we can only place one session’s pre-run Freesurfer outputs.
  • This is because Freesurfer’s outputs (folder names: label, mri, scripts, stats, surf, tmp, touch, trash) are the same for each session.
  • So, when I copy those outputs into /out/freesurfer/sub-999 there is a duplicate naming issue.

The question:

  • Does fMRIPrep allow for the use of two separate Freesurfer inputs for a single participant?
  • I have tried splitting the freesurfer folder (/out/freesurfer/sub-999) into sessions (/sub-1/ses-1 and /sub-1/ses-2) according to BIDS, but that caused an error.

Any help would be much appreciated.

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