SHELL

masking

#!/bin/sh

# Make an inverse binary image mask (switch the 1s and 0’s)

# Create the inverse mask (Mark Jenkinson's approach. Very clever:
# Multiply by negative 1, then add 1). Make sure you pass in a binary mask)

fslmaths mask -mul -1 -add 1 -bin mask_inverse 

# OR use -binv flag

fslmaths mask -binv mask_inverse