====== Thalamus ======

===== MRSI =====

Interest in Thalamus from Sarpal, via FC:
> [[:brain:NAAG]] is meant to modulate glutamatergic activity, so quetion was whether this predicts thalamic functional connectivity 
> running a seeded [[brain:functionalconnectivity]] analysis on the thalamus and regressing voxelwise values vs NAAG seemed like a relatively easy thing to check


===== Segmentation =====

For [[tools:freesurfer]] segmentation, see [[https://freesurfer.net/fswiki/ThalamicNuclei|segmentThalamicNuclei.sh]]. 

==== 7T ====

In [[:grants:7t:mr|]], ''/Volumes/Hera/Projects/7TBrainMech/scripts/mri/FS/020_segThal.bash'' has <code>
# run thalmus segmentation with FS7.2
# 20230313 ... for OR

STATS=thalamic-nuclei.rh.v12.T1.stats
SCRIPT=segmentThalamicNuclei.sh
</code>

As of 2025-09-09, 275 have ''ThalamicNuclei.v12.T1.mgz'' segmentation output files.
<code>
ls  /Volumes/Hera/preproc/7TBrainMech_rest/FS7.2/highres/1*_2*/mri/ThalamicNuclei.v12.T1.mgz|wc -l
275
</code>