Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 9:45 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Grey Matter Intensities

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I think these are not grey matter but cortical parcellation. 

FSL can output grey matter segmentation but I do not think freesurfer has such an output.

In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.

On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

Recon-all outputs these 3 aparc aseg volumes:

aparc.DKTatlas+aseg.mgz

aparc.a2009s+aseg.mgz

aparc+aseg.mgz

Are these what you are looking for? They should work the same way as aseg volume.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI
Sent: Tuesday, February 20, 2024 3:22 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Grey Matter Intensities

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Hi Freesurfer team, 

Recon-all output  shows the white matter volumes and white matter  intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.

Thank you.

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