you will have to binarize it first, eg, mri_binarize --i inputimage.mgz --min threshold --o binary.mgz, then run mri_segstats --seg binary.mgz --id 1 --i inputimage.mgz --sum sum.dat

On 2/7/2024 8:55 AM, Huang, Yujing wrote:

I think mri_segstats –i option will do that - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Best,

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *ERNEST KISSI *Sent:* Wednesday, February 7, 2024 8:12 AM *To:* Freesurfer support list Freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Calculation of MRI intensity

*        External Email - Use Caution *

Hi Freesurfer Team,

Please I want to calculate the mean intensity of a skullstripped MRI image. I do not want to use recon-all because I do not want to parcellate or segment it. Is there such utility or function in freesurfer?

Thank you.

Sincerely,

Ernest Kissi Kontor.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer