You have to register the atlas to each individual person's space. You can do this with
mri_coreg --mov atlas-template-brain.nii.gz --targ brain.mgz --dof 12 --reg reg.lta
Then map the atlas to the subject's space
mri_vol2vol --mov atlas.nii.gz --targ brain.mgz --reg reg.lta --interp nearest --o atlas-in-subject.mgz
You can run run mri_segstats to get volumes
mri_segstats --seg atlas-in-subject.mgz --excludeid 0 --sum summary.dat

On 1/16/2023 2:17 PM, Beatriz Cavendish wrote:

External Email - Use Caution

Hi all,

I would like to know how to quantify the regional volume using an external atlas. I already ran the recon all command and now I want to quantify the volume not with the default Freesurfer atlases, but a specific atlas that is in the MNI space. Should I transform the atlas to each subject's native space before quantifying? How should I do it? Then how do I quantify it and make sure it was done correctly? Could you provide me with command line suggestions? And if I wanted to work with everything on the MNI space, how would the code be like?

Also,

Best,

--

Beatriz Araújo Cavendish, MSc

PhD student | Psychologist

University of São Paulo

São Paulo/SP - Brazil
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