External Email - Use Caution
Hello, I am newer to Freesurfer and have been unable to find a reference on how to extract the volumes/voxels of the hierarchical segmentations using FS 7.1 (e.g, from rh.hippoAmygLabels-T1-T2.v21.CA.mgz).
I am trying to compare manual segmentations to those generated by Freesurfer and the closest hierarchical segmentation is "CA". However, because the volume output (i.e., from quantifyHAsubregions.sh) does not seem specific to a given hierarchical segmentation, I am unsure how the molecular layer is being assigned for the "CA" segmentation given these voxels are assigned to the nearest voxel that isn't the molecular layer or background.
Any guidance on how to extract volumes that reflect the "CA" segmentation would be greatly appreciated.
Best regards, Kelsey Canada