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Let's say the red spot is overlay.nii.gz 1) convert aparc+aseg from mgz to nii.gz using: mri_convert aparc+aseg.mgz aparc+aseg.nii.gz 2) create mask between overlay and the atlas using fslmaths: fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz overlay_overlap.nii.gz 3) use fslstats (or mris_cacl) to compute volume: fslstats aparc+aseg.nii.gz -k overlay_overlap.nii.gz -V this output #voxels and volume
Alternatively, you might consider mri_seg_overlap https://secure-web.cisco.com/1yEdORqlIEup_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJa...
On Fri, Jun 16, 2023 at 10:37 PM parsatad@student.ubc.ca < parsatad@student.ubc.ca> wrote:
External Email - Use CautionHello,
Hope you are doing well. I'm new to freesurfer so I was wondering if you could help me out with something please.
I'm looking for a simple way to find the size (i.e. volume in mm3) of overlap between a particular label (1027 ctx-lh-rostalmiddlefrontal) ) in an aparc+aseg file and a NIfTI volume file that can be overlayed on the aparc+aseg file. Please look at the attached file for a better visualization of what I'm describing.
I'd really appreciate it if you could point me in the right direction.
Thank you,
Parsa
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