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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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:
External Email - Use Caution
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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