Hello FreeSurfer Developers,

I am trying to generate a connectome in MRtrix3 using FreeSurfer parcellations and segmentations. I am specifically interested in the subregions of the thalamus and noticed that the newest version of FreeSurfer (7.3.1) has added segment_subregions.

This command runs on my M1 mac without error and successfully outputs ThalamicNuclei.FSvoxelSpace.mgz, ThalamicNuclei.mgz, and ThalamicNuclei.volumes.txt.

I am wondering if it is possible to generate a file similar to aparc+aseg.mgz that is generated in recon-all, but with thalamic subregion segmentations included.

I was thinking that the following steps could possibly work:

Run recon-all
Run segment_subregions thalamus
mri_surf2volseg:

mri_surf2volseg --i ThalamicNuclei.FSvoxelSpace.mgz --fix-presurf-with-ribbon ribbon.mgz --o aseg_new.mgz \

--lh-cortex-mask ../label/lh.cortex.label \

--rh-cortex-mask ../label/rh.cortex.label \

--lh-white ../surf/lh.white --lh-pial ../surf/lh.pial \

--rh-white ../surf/rh.white --rh-pial ../surf/rh.pial

merge seg --src aseg.mgz --merge aseg_new.mgz --o aseg_all.mgz
mri_surf2volseg --i aseg_all.mgz --label-cortex --o aparc+aseg_thalamus.mgz --lh-annot ../label/lh.aparc.annot 1000 --rh-annot ../label/rh.aparc.annot 2000 --lh-cortex-mask ../label/lh.cortex.label --rh-cortex-mask ../label/rh.cortex.label --lh-white ../surf/lh.white --lh-pial ../surf/lh.pial --rh-white ../surf/rh.white --rh-pial ../surf/rh.pial

I appreciate your time, and I look forward to hearing from you.