You have to run recon-all through to the end. You can then extract a GM
mask from that. You will need to register your PET image to the
anatomical (mri_coreg), map the PET into the anatomical space, then use
mri_segstats to compute the mean PET in the GM mask. Alternatively, you
may want to use PETsurfer (search for it on the wiki).
On 2/6/18 11:06 AM, Hanna Vasilevskaya wrote:
Hello FS team,
I am new to FS and using version 5.3 on a Mac. I have minimal
programming background and this might be a very easy question, however
I was not able to find a similar one in the archive.
I have T1 MRI images from multiple subjects and I need to extract the
brain gray matter mask (just cortical regions, without cerebellum). I
will then use this mask as an ROI to extract PET activity.
Would you happen to know a way for this?
Thank you greatly,
Anna
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