Hi Kelsey, The volumes are derived from the probabilistic segmentation at the finest level of detail, so there’s no direct mapping to the different hierarchical segmentations. Your safest bet is probably to count the number of voxels in the hard segmentation and multiply by the volume of the voxel. Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kelsey Leigh Canada kcanada@umd.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, August 30, 2020 at 10:17 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Extracting hierarchical hippocampal segmentation volumes

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