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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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.
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