Convert the surface-based parcellation to volume-based


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
–o /local_raid/data/hjiang/annot/500.aparc.mgz
–annot 500.aparc

mri_label2vol --seg /local_raid/data/hjiang/annot/500.aparc.mgz
–temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz
–o /local_raid/data/hjiang/annot/500.aparc.nii.gz
–regheader $SUBJECTS_DIR/fsaverage/mri/aseg.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.