SHELL

fslmaths subtract

#!/bin/sh

# Subtract one mask from another.  Binarize the resulting difference
# with -bin to get rid of negative numbers. See the jaccard index to expand on this use.

fslmaths mask1 -sub mask2 -bin mask_diff

fslmaths subtract

#!/bin/sh

# Make an empty image (same dimensions as input image). 
# See also fslhd.

fslmaths img -sub img empty_img # subtract the image from itself
# OR
fslmaths img -mul 0 empty_img  # mulitply the image by 0