What is the size of your VOI.mgz? Ie, if you run
mri_info --dim VOI.mgz
It should be 1 1 1, meaning that it is a single voxel
On 2/22/2022 3:27 PM, Brown, Alexander wrote:
External Email - Use Caution
Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the
terminal output. The output files generated (i.e, cortex.mgz) are the
partial volume segmentations for the whole brain. There were no output
files that segmented the VOI mask (VOI.mgz). Maybe I didn't specify
the input correctly? I inititally recieved errors saying the
--regheader flag needs 2 arguments, so I used --regheader <subjid>
<path to VOI.mgz>
Now that the tissue maps are generated, Another option I considered is
using mri_segstats to extract tissue composition stats from the VOI by
using the mri_compute_volume_fractions output volumes (i.e.
cortex.mgz) as the segmentation input files and using the VOI.mgz as a
mask. However, I am not sure how to address calculating the partial
volumes using mri_segstats in coordination with the VOI.mgz mask.
Thanks again for all the help.
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 9:21 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
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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, February 21, 2022 5:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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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