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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lauren Taylor
<l...@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
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