pierremegevand
commented
1 week ago Hi Timna,
FreeSurfer also creates parcellated volumes, in addition to the parcellated surfaces. In the subfolder 'mri' of a given FreeSurfer output, you will find the following MRI volumes:
- aparc+aseg.mgz contains the Desikan-Killiany parcellation of cortex
- aparc-a2009s+aseg.mgz contains the Destrieux parcellation
- wmparc.mgz "propagates" the DK parcellation to the underlying white matter
For more info on how these volumes are computed, see the FreeSurfer documentation:
- https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg
- https://surfer.nmr.mgh.harvard.edu/fswiki/wmparc
You just need to convert the .mgz into a .nii file, e.g. using FreeSurfer's mri_convert function.
I hope this is useful, let me know.
Hi! I saw in the wiki that one could upload a parcellation file of type nii, but, from what I understand, the output of freesurfer is .anot files for the parcellation. I wondered if I might be missing something and the files do exist in the freesurfer output, or if they are not the output of freesurfer how do you recommend getting them, or converting the .anot files to .nii.
Thanks!