Hi Hannah,

It would be hard to use the mask script, as the script needs FSL-style warp data (needed to warp MNI152-standard-space masks to anatomical space).  You could do the same type of thing as the script.  Basically, you would need to:
1. Segment the anatomical
2. Warp standard masks of ventricles and white matter from MNI152 space to anatomical space
3. Mask the segmentation output from #1 with the warped masks from #2

Best,
Jeff