Structural brin MRI preprpcessing

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Hello pals,

the question is about an automated tool for structural MRI data preprocessing.
we are working with sMRI data with several 3D protocols - T1w, T2w, and Flair or DWI typically. if there is an option to process all of them in fmriprep pipeline?

As far, as I observe, T1 can be processed in Freesurfer of FSL or fmriprep. ThenT2 can be treated in FSL and fmriprep, yet it will choose imagery with the best resolution among T1 and T2.

So the question in a nutshell: if you are working with multimodal sMRI data, what tool do you use for pre-processing (scull-stripping, normalization, atlasing)?

p.s. happy new year to all!

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The structural portion of the fMRIPrep pipeline has been split out into sMRIPrep (https://github.com/nipreps/smriprep/). One thing that isn’t currently done, but there’s an open issue for, is to register the T2w/FLAIR images to T1w.

For DWI, there’s a related effort called dMRIPrep, which I believe is still somewhat of a work in progress, and another similar tool called QSIPrep.

If you have any interest in trying these out, reporting any issues, and potentially contributing any missing functionality for your use case, that would be great!

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