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-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 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:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1SZ_ZwxUHUoHqP332XFGWKlV1rBGVZpWfjoGbMwovH8RMj2XdDYrM9GgfKAiqt0TrmkE3Gwe0p6N2B-5ZMPuLVZPJXyW0NKljySOhcBqh9dOUag4g2j3zWx5OSaGYVqNRqpWcQ42YvXBRMppsZDyLzqBQ81UYPC_sooTdOYpHFKKb0XXVAHa7OFCexOXG_2VMsjR-B_RlbEy-a8Eog3lcJSSB-mGFDIN8GzE92BZShp4UQHnygF8s7SK9jO7EgXqWIQbb1H5LGnm-TO4arAF8nUF_stbNshv42dAMfwZziQIKRoi36_H65-ZZVLJe5Z-mQrn57AEHzksDP0bz7gLlhA/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257Cb780495e7cc04454891108d9f591850c%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637810827623402419%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DS6AoUqej6ir9sOSfR7h%252Bx0phctkv0%252BTzwCB7XwS2Tww%253D%26reserved%3D0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer