I am trying to convert the surface-based parcellation (.annot file) to volume-based parcellation, and calculate the functional connectivity based on the volume-based one. I used the following command to do that:
mri_aparc2aseg --s fsaverage --new-ribbon
mri_label2vol --seg /local_raid/data/hjiang/annot/500.aparc.mgz
But the generated nifti file seems not to cover the whole gray matter when compared to the MNI template. (The regions circled by blue lines are missing.)
What I want ideally is like this.
I would appreciate it if you could give me any help with this. Thanks a lot.