Is it possible to perform white matter parcellation inside fmriprep by further specifying recon-all?

Summary of what happened:

I am using fmriprep with the recon-all command and I am getting aparc-aseg segmentations and everything works as expected and I have my nice cortical segmentations. I also have left/right white matter labels for the whole hemispheric white matter. I would like to further parcellate the white matter into smaller WM regions, so to associate the white matter hyperintensities for each white matter region to the corresponding cortical regional activity in the DK atlas. From what I see on freesurfer - but I don’t have any previous experience with it, so I might be wrong - it looks like this can be accomplished in recon-all. I was wondering if there is any way to obtain the white matter segmentation already inside fmriprep by somehow changing the input of recon-all. Otherwise, is there any other advisable solution instead of re-running the whole recon-all pipeline after fmriprep is done?

Thanks a lot!


Fmriprep v. 21.0.2

Environment (Docker, Singularity, custom installation):


Hi @Riccardo_Leone, could you describe what you would do with FreeSurfer if you were running it without fMRIPrep? I can help figure out what to do with an fMRIPrep-run reconstruction.

Hi! Sorry for the late reply, I ended up using a completely different method using the BCBToolkit.