adding task fmri stream / 3dDeconvolve / to micapipe

MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

http://micapipe.readthedocs.io

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adding task fmri stream / 3dDeconvolve / to micapipe #24

Closed neuroimagingdatascience closed 1 year ago

neuroimagingdatascience commented 2 years ago

might be great to add a task fmri stream to micapipe at one point in early 2022. We discussed this with some of you already and it may be a slight variation of the already existing rest fmri stream, and perhaps include afni's 3dDeconvolve to get beta time series that would then be mapped to the surfaces (instead of / or in addition to the preprocessed task based time series). https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDeconvolve.html

Shoobidoo commented 2 years ago

I'd been working on that a while back. I have a work-in-progress version of a task fmri script with 3dDeconvolve.

rcruces commented 2 years ago

Task fMRI stream is under development on the devTask branch
3dDeconvolve is not implemented yet.

rcruces commented 1 year ago

The task processing can be perform now with the multi-acquisitions proc_func module. It will do motion correction, high-pass filter, geometric distortions, ICA cleaning, with FIX or tenada (if the data is multi echo https://tedana.readthedocs.io/en/stable/multi-echo.html) and plot the results to the surface. Since, 3dDeconvolve depends on each of the task we recommend to run the proc_func and then do the post processing with the clean func output after, either on a surface level or at the volume level.

see the version 0.1.5 of the pipeline for more information