Create MTR images using FSL

This assumes that the MT off and MT on images were acquired on a Philips MRI scanner using two dynamics using the MT option, and that the converted Analyze of NIFTI images are in one file consisting of two volumes, with a base filename of set10. If the MT off and MT on images are in separate Analyze files then skip the first line and use these files rather than the vol files created by avwsplit. The file containing the MTR images is called set10_mtr.

avwsplit set10 set10_vol
bet2 set10 set10_brain -f 0.2 -m
avwmaths_32R set10_vol0000 -sub set10_vol0001 -div set10_vol0000 -nan -thr 0 -mas set10_brain_mask set10_mtr
rm set10_vol*