Hi Anil,

I think mri_mask will do this.

Bruce

On Tue, 19 Feb 2008, Anil Roy wrote:

Hello All,

I used mri_binarize to create stg masks (inclusive of gray and white matter).

I'm trying to take this a step forward to see if I can extract the actual brain region encompassed by the mask - in other words, is there a way to cut out the portion of the brain that the mask encloses. So instead of this being a binary mask with stg =1 and everything else 0, could we get everything else to be 0 and stg to remain as it is.

The main reason I want to do this is that I have some other software that can create intensity histograms for such extracted regions and also perform some other analysis.

Thanks,

Anil.