How to create a 3d mask from an image

Hi, Ok the problem I am having is this. I have a 3d matrix, which has a brain in it. I want to segment the brain and create a mask (1 = brain, 0 = outside). Now I know there are 2d segmentation tools (take each slice and segment it) but the problem my teacher wants to segment the brain in 3d. So I need 3d segmentation not 2d segmentation.mask. Anyone got any tips/programs which can do this?

Regards

Below is the brain taken in 3 different directions, ortho, coronal, longitudinal e.g

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[Saurabh Sakpal]