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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. 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
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