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