Registering a ROI atlas to native space with fMRIPrep


We’d like to perform some network analysis in subject’s native space using the ROIs of the Brainnetome atlas as nodes. To this end, we’d need to transfer the atlas from the MNI space to the native space (either t1w or bold space). Is there a way to do this with #fmriprep?

I noticed that fMRIPrep’s anatomical workflow outputs the t1w → MNI transform and its inverse (called std2anat_xfm). So, we can take this transform and write a script to apply it on the atlas. However, I wonder if this could be done inside fMRIPrep without any additional scripting.

So far, my best guess would be running the anatomical workflow without skull stripping or surface reconstruction, giving the Brainnetome template as input and subject’s native space as output space, that is, something on the lines of

fmriprep <input> <output> participant --participant-label <subjID> --anat-only --skull-strip-t1w skip --fs-no-reconall --output-spaces <native space>

Could this work? If so, how to create the <native space> template? I suppose it should be created as a custom standard space under TemplateFlow? Is there a way to do this without committing to the TemplateFlow repo? TemplateFlow’s own tutorial seems to be for publishing only.

Thanks for your help!



Transforming parcellations in this way would fall outside the scope of fMRIPrep.

Yup! Since you’ll be working with label / atlas data, a simple nearest-neighbor interpolation should work just fine when you apply the transform.


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