Open ChristianNSchmitz opened 9 months ago
Hi @ChristianNSchmitz, yes this is on our roadmap for 2024. This behavior is currently implemented in nibabies, so we expect to be able to implement it in fMRIPrep.
Hello! Have any of you already tried using the FreeSurfer outputs with a longitudinal structure in fMRIPrep? I am very interested in using it in that way. Could you clarify which should be the FreeSurfer folder structure?
@Beatrizfg20 yes, I recently added this feature here https://github.com/nipreps/fmriprep/pull/3142 / https://github.com/nipreps/smriprep/pull/393 to just do that. I applied this on our dataset, though I used smriprep first steps on the raw T1w/T2w images before feeding these to freesurfer cross-sectional (as it was more robust for skull-stripping), then ran the base and longitudinal templates and provided these to smriprep anat-only to then use it with fmriprep.
What would you like to see added in fMRIPrep?
Dear fMRIPrep-Team,
we are currently working with longitudinal data and would like to use the strucutral freesurfer-output for further analysis. Unfortunately, fMRIPrep creates an average image of all T1 weighted images and only the tweak with the flag --bids-filter-file enables the separate analysis of different sessions. Thus, we would like to ask you if a separate structural analysis of different sessions would be possible.
Best, Christian
Do you have any interest in helping implement the feature?
Yes
Additional information / screenshots
No response