Enable longitudinal structural analysis

[ChristianNSchmitz]

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

[effigies]

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.

[Beatrizfg20]

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?

[bpinsard]

@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.