To get skull, you can run samseg (in v7). The other stuff can be segmented with CHARM (https://www.sciencedirect.com/science/article/pii/S1053811920305309). CC'ing Oula in case he wants to weigh in

On 8/21/2020 4:38 AM, mudassar liaq wrote:

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Basically I want to segment all the parts of a Brain MRI (not only the brain in MRI but also skull and other muscles that do also appear regularly). I am able to generate a mask for everything but brain

But I want every part that appears in Brain MRI to be labeled as well ( all other muscles and skull ).

Thanks and Regards,
On Thu, Aug 20, 2020, 10:54 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
can you be more specific?

On 8/20/2020 4:37 AM, mudassar liaq wrote:
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Hi,
(A but of a dumb question but) Is there any way we can also have skull also labeled () along with the brain parts in MRI output?

* Skull mentioned by white arrows

Thanks and Regards,
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