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Enable longitudinal structural analysis #429

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ChristianNSchmitz opened this issue Nov 15, 2023 · 3 comments · May be fixed by nipreps/fmriprep#3265
Open

Enable longitudinal structural analysis #429

ChristianNSchmitz opened this issue Nov 15, 2023 · 3 comments · May be fixed by nipreps/fmriprep#3265
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effort:medium Estimated medium effort task freesurfer FreeSurfer related improvements and issues impact:high Estimated high impact task

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@ChristianNSchmitz
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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
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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.

@tsalo tsalo linked a pull request Mar 29, 2024 that will close this issue
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@Beatrizfg20
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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?

@oesteban oesteban transferred this issue from nipreps/fmriprep Apr 9, 2024
@oesteban oesteban added freesurfer FreeSurfer related improvements and issues effort:medium Estimated medium effort task impact:high Estimated high impact task labels Apr 9, 2024
@bpinsard
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bpinsard commented May 7, 2024

@Beatrizfg20 yes, I recently added this feature here nipreps/fmriprep#3142 / #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.

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effort:medium Estimated medium effort task freesurfer FreeSurfer related improvements and issues impact:high Estimated high impact task
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Add --session-id parameter and support longitudinal output structure tsalo/fmriprep
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@effigies @oesteban @bpinsard @ChristianNSchmitz @Beatrizfg20