How to extract 3D patches from only region within the brain and not include the background

I have a 3-D MRI image of the brain. Some part of the image is the background which I don't need since I want to extract patches from only the region with the brain tissue. Is there a way to limit my patch extraction to the brain region without extracting from the surrounding black background.

[Santiago Silva]

When you say extract the region, do you mean the size of the block extraction? or how to extract a region (with a mask, e.g.).

[Image Analyst]

How are you extracting? By thresholding? Then why would any of the black surrounding stuff (air) be extracted???