If you want to do an ROI analysis using FS-based ROIs, you should do that at the individual level. Resample the PET to the anatoimical space, then run mri_segstats passing the PET with --i and using --seg to spec the segmentation. If you really want to do it in MNI305 space, then it is the same thing just using the MNI305-based (2mm) segmentation

On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

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Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask.

How do I extract mean intensity within all of the subcortical ROI?

Thank you!

Warm regards,

Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865 | Fax: 310-315-4069
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