You can follow the examples described here

https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/project_to_individual

From: Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Thursday, March 12, 2026 4:07 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: use of a custom annot for mri_segstats

I think you will need to map the atlas to the individual subject space.

For example,

mri_surf2surf --srcsubject fsaverage --trgsubject <subject_id> --hemi <lh/rh> --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.Schaefer2018_400Parcels_17Networks_order.annot --tval $SUBJECTS_DIR/<subject_id>/label/lh.Schaefer2018_400Parcels_17Networks_order.annot

From: Simone Cauzzo <cauzzo.simone@gmail.com>
Sent: Wednesday, March 11, 2026 11:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] use of a custom annot for mri_segstats

        External Email - Use Caution        

Hi all

I am running Freesurfer 7.4

I am trying to extract QSM values at different cortical depths, and obtain statistics for the 400 Schaefer regions.

my code is 

mri_vol2surf --mov [QSM coregistered to orig_nu.mgz ] \
             --regheader $sub \
             --hemi lh \
             --surf white \
             --o outputsurf.mgh \
             --projfrac 0.2

mri_segstats --annot subjid lh 400Parcels_Yeo2011_17Networks \
             --i outputsurf.mgh \
             --sum outputstats.stats

I get the following errors

Reading annotation $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot
error: No such file or directory
error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match
 ... trying local annot
error: No such file or directory
error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match

The annot file is there, I checked, and that's verified by the fact that apparently it knows how many vertices are there. Moreover, it totally worked when I tried this command to extract anatomical stats from the same parcel

mris_anatomical_stats -a $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot -f $SUBJECTS_DIR/$sub/stats/$hemi.$parc.stats $sub $hemi

Do you have any idea of what is going on?

The volume [QSM coregistered to orig_nu.mgz ] was created by applying the QSM 2 T1 rigid transform with ants antsApplyTransform, with orig_nu.mgz as reference volume, which provided a new QSM volume that looks aligned to orig_nu.mgz and on the same grid. It is not a problem of this file since I tried producing an mgh file with orig_nu.mgz as --mov volume and the error persists.

Thank you for your help

Simone Cauzzo