Hi Freesurfer Team, I'm attempting to calculate the volume of hippocampal subfields (e.g., CA1-3, DG) in the anterior (head), middle (body), and poster (tail) subregions of the hippocampus. I have manually determined the boundaries for head/body/tail using standard anatomical landmarks and included these updated labels in the aseg files. I am attempting to use those (head/body/tail) volumes as masks when generating the hippocampal subfield (CA1-3, DG) volumes. Could you confirm that these are the correct steps to this end?
*Note.* Based on the prior literature, the asegs were ac-pc aligned in AFNI to determine unbiased boundaries for head/body/tail.
mri_binarize --i aseg_acpc_antpost.mgz --match 91 --o Lhead_mask.nii
#LHead=label 91 mri_segstats --seg lh.hippoSfLabels-T1-T1T2.v10.1mm_acpc.nii --mask Lhead_mask.nii --excludeid 0 --pv norm_acpc.nii --sum ../stats/substats_lhead
The outputs appear reasonable (i.e., the volumes generated by mri_segstats with the mask are smaller than without the mask), but I wanted to ensure that this is the appropriate method to generate what I'm looking for.
Thank you in advance for your help!
Sarah