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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

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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 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-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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