Is it in the surface annot mapped to native space?

On 4/14/2025 11:22 AM, Simone Cauzzo wrote:

External Email - Use Caution

Dear support I want to put the Yeo 400 annotations on my recon-all output and produce a volume. I'm using the following commands:

mri_surf2surf --srcsubject fsaverage --trgsubject subj[..] --hemi rh --sval-annot [...]/Yeo_fsaverage/label/kong17/rh.400Parcels_Kong2022_17Networks.annot --tval [...]/rh.aparcYeo.annot

[same for LH]

mri_surf2volseg --o [...]_aparc+aseg_yeo.mgz --label-cortex --i mri/aseg.mgz --srcmri/aseg.mgz --threads 4 --lh-annot label/lh.aparcYeo.annot 0 --lh-cortex-mask label/lh.cortex+hipamyg.label --lh-white surf/lh.white --lh-pial surf/lh.pial --rh-annot label/rh.aparcYeo.annot 200 --rh-cortex-mask label/rh.cortex+hipamyg.label --rh-white surf/rh.white --rh-pial surf/rh.pial

The annotations come from Yeo_fsaverage/label/kong17/lh.400Parcels_Kong2022_17Networks.annot as downloaded from the link in the paper published.

For some reason, left hemisphere region 17networks_LH_DefaultC_PHC_2 is not present in the resulting volume. The region is just set to zero as if it was masked out. I thought about something wrong with the recon all output but this happens for all my subjects, and the recon-all output looks ok.

Am I missing something?

Simone Cauzzo

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer