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brain:thalamus [2025/09/09 16:16] – created willbrain:thalamus [2025/09/09 16:23] (current) – [MRSI] will
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 ====== Thalamus ====== ====== 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]].  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> 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 STATS=thalamic-nuclei.rh.v12.T1.stats
 SCRIPT=segmentThalamicNuclei.sh 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> </code>