Hi Lauren - What you want is to replace the thalamus labels in aparc+aseg.mgz with the thalamic nuclei labels. This is a bit less straightforward than it may first seem because the outer boundaries of the thalamus in the two segmentations are not necessarily the same. However, we've implemented this replacement in the TRACULA pre-processing stream, so you can check out the trac-preproc script to see how it's done and grab the relevant commands.

Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lauren Taylor ltay@uw.edu Sent: Monday, August 8, 2022 2:57 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentation of thalamic nuclei: possibility of generating connectome

External Email - Use Caution

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.

Thanks,

Lauren Taylor