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

,
5

Hi @Arsh,

No, that would not work. fMRIprep expects outputs to be in folders as SUBJECTS_DIR/sub-xx/. It does not expect session organized freesurfer inputs and will not look in them. What you would need to do is something like

fastsurfer/
└── ses-BAS1
    ├── sub-A00079302
    │   ├── label
    │   ├── mri
    │   ├── ...
    ├── sub-XX
    │   ├── label
    │   ├── mri
    │   ├── ...
└── ses-BAS2
    ├── sub-A00079302
    │   ├── label
    │   ├── mri
    │   ├── ...
    ├── sub-XX
    │   ├── label
    │   ├── mri
    │   ├── ...

and then in your fmriprep command set the --fs-subjects-dir to /path/to/fastsurfer/ses-XX.

You are correct about the filter file though. Hope it works for you!

Best,
Steven