macaque brain segmentation

[SylvainT]

Hi all,

I'm trying to segment some macaque brains... All I'm looking for is to get a mesh of the outer skull and a mesh of the brain surface (I don't need a grey/white segmentation)

Do you guys have any general advice??? Can I try to use the pipeline (after un-clicking the un-necessary steps), or do I need to perform all the steps one by one?

Other than this, I have two practical questions to start with:

1. the macaques were in sphinx position when the T1 was acquired. Do I need to artificially rotate the volume so that it looks like it was acquired in a "standard orientation"?

2. one of the macaques has a large right/left dissimetry in its skull (a large, very large, amount of bone exists on the right, but not on the left, the left side being "normal" for that matter); will this affect any of the processing steps (which might rely on some symmetry assumption)?

Thanks in advance for any help,

Sylvain

[Jean-Francois Mangin]

If you have only one dataset, the best is that I process it for you.
I played with a lot of monkeys last years, various problems can occur...
For instance stupid things like having muscles bigger than brain, which I did not planned...
I will have to set up processing lines for monkeys I am afraid, do not know when.
If you have a lot of them, we need to talk more...