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:
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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
*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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@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 WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. 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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