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Good luck. It requires a 7T to separate the compacta and reticulata. Localizing the the substantia nigra is impossible with standard MPRAGES but can be done if you modify the sequence or use a adequate T2 . There are papers that discuss how to localize it you do not need FreeSurfer.

On Mon, Mar 6, 2023 at 4:57 PM Christian Owen cowen314@gmail.com wrote:

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Hi,

The latest post I could find about substantia nigra segmentation in FreeSurfer is from May 2020 https://secure-web.cisco.com/1kbKgUj7tgWerg-kNskO0E4pbYddAh99-3abcyl688pSr522HGfljzK8Vg4SNMuYr1Re0HWn70-luj0Zzcnr82x_lSUWwV4aI18Nm1oXzKf2dbtRMimEn_Y-IUUPqisF8FJzamdL_zEhIJ7TjwB0DFoVBD9qQROzryqS6T7F-vngpBezA3DNc86hQBa5kidKRPzit-26Vi2sMP5KuRqZNwS7dKQ7oBvVh1AQ0gBqIb3ErPoJx3CYBiwW9aiEkSmbR_LDBqWH_A7-dgzmJvFbbchq2K6PaLGbm0zf1L5CyK4HJ4BFVg00hqKbyH_QUKGHjzBubOr-kXKehbegvMQt9AA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66192.html. As of that post, it was not possible. Is it still not possible? If that's the case:

• is substantia nigra segmentation on the roadmap?
• is there anything a software engineer could do to help make it happen? I

cannot promise any resources atm, but there's a chance we could help out (if it turns out to be enough of a priority).

Best, Christian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1SWl-V7iU1qReuhyJbW2nU6wqQ20sPDjAMo6G3ECMX1IbuW... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1BAW_kjXHQVyei7p3Ft1p3-XL3wc0CFxVpEe5a4-91NJOaL... < https://secure-web.cisco.com/1BAW_kjXHQVyei7p3Ft1p3-XL3wc0CFxVpEe5a4-91NJOaL... .