You are right, it does not make sense to try to pull the CC subregions into surface space as they are volume labels. You recommended: "As for getting them into MNI152, you could just run recon-all on the MNI152." I am not following, can you elaborate on how I would run recon-all on the MNI152? And once I do that, how would I extract the CC subregions to be used in FSL?

For background, what I would like to do is take the CC subregions in FreeSurfer and convert them into MNI space to be used as ROIs in FSL DTI analyses. We found some volumetric differences of FreeSurfer CC ROIs, and now we want to pull those same ROIs into FSL for our DTI analyses.

Best,

Jessica

From: Hua, Jessica
Sent: Tuesday, March 8, 2022 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Straub, Kelsey (MU-Student) <ktsfk2@mail.missouri.edu>
Subject: Extraction of CC Labels and Conversion to FSL MNI Space

Hi FreeSurfer,

I am trying to extract CC subregion labels from aparc+aseg.mgz (ids: 251-255) into a format that is compatible with MNI space in FSL. I was planning on extracting CC labels and then converting the labels from fsaverage space to MNI space. I first tried to extract the 5 separate CC labels using the command: mri_vol2label --c aparc+aseg.mgz --id 255 --l 255.label. When viewed in FreeView, the labels were spotty looking. Did I do this mgz to label extraction correctly?

And also do you have a recommended code to convert FreeSurfer CC subregions into MNI space ROIs for FSL?

Best,

Jessica