Look in the recon-all.log file for the command that generates the aseg.stats file. Use that command but change aseg.mgz to whatever your mask is (and change the output). Don't include the LUT on the command line.

On 11/1/17 10:24 PM, Ehsan Tadayon wrote:

Hello FS experts, 

I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz? 

thanks. 

Ehsan

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