External Email - Use Caution Dear Freesurfer community,
Our group is using the new FreeSurfer 6.0 (dev) subcortical segmentation scripts on HCP data (Freesurfer 5.3) segmentHA_T2.sh segmentThalamicNuclei.sh We have successfully segmented the three structures 1. lh.hippoAmygLabels-T1-T2_seg.v21.mgz 2. rh.hippoAmygLabels-T1-T2_seg.v21.mgz 3. ThalamicNuclei.v10.T1.mgz We have found that there is significant overlap (see attached) bilateraly at the tail of the hippocampus. This makes some sense anatomically but we need to define these areas as a unique structure. Has anyone dealt with this overlap ROI issue before? Thanks Juan Sanchez - Pena
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