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I'm not sure what you are trying to do exactly. It looks like you want to get cortical volumes of regions in BN_Atlas. Please elaborate.

On 4/20/2023 12:52 AM, Garrett Tan wrote:

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Hi FreeSurfer Experts,

I am using Brainnetome Atlas in FreeSurfer to calculate the brain volume. The cortical regions are done smoothly by using mris_ca_label->mris_anatomical_stats with materials on https://secure-web.cisco.com/1p7TY1frW67uqViolqd97Sub3WUDGgPjPK0_YAEmmtEENBB... However, when I was trying to get the volume of subcortical regions (the hippocampus, amygdala, thalamus, and basal ganglia), they are excluded since the ?h.cortex.label files do not include them.

My plan was to use aseg.mgz to get each subcortical regions and do the same procedure as for the cortical regions. However, mri_ca_label did not allow me to create .annot from BN_Atlas_subcortex.gca from Brainnetome website. So I continued using mris_convert to convert .gca to label.mgz, and I am stuck here. Is there any way to get the subcortical regions’ .gcs file, or even an easier way to calculate the volume of subcortical regions in brainnetome atlas from FreeSurfer?

Best, Garrett

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