If you already have the VOI that is aligned to the mprage via the geometry in the volume header, then you can use mri_compute_volume_fractions to compute the composition; specify --regheader subject. To be clear, this assumes that the VOI is a single voxel in a "volume" (eg, nii or mgz) and when you run
freeview orig.mgz VOI.mgz
you see the VOI in the right place on the orig.mgz. When these conditions are met, mri_compute_volume_fractions will give you what you want. One last thing is that volume_fractions will give you another single-voxel "volume" as output. There are several ways to get the value out, the easiest is probably matlab, something like
a = MRIread('singlevoxvol.mgz');
a.vol % will give you the value

On 2/21/2022 6:57 PM, Brown, Alexander wrote:

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Yes, it is MRS. 

Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?

Thanks,
Alex    

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Monday, February 21, 2022 5:25 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
 
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I don't know what an svs is. Is it like MRS?

On 2/21/2022 5:51 PM, Brown, Alexander wrote:

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Hello,

I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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