Hi Varsha,
I need to look into the mrstats behaviour both for this and another similar issue. But you’re right in that the CSF mask derived during the dwi2response msmt_5tt algorithm shouldn’t be empty. My suspicion is that derivation of the 5TT image has somehow gone awry, and the crashing dwi2response call is a downstream effect. Are you able to check that your 5TT image conforms to the expected format and contains the expected information? If you’re unsure, you could run the 5tt2vis command and post a screenshot of the resulting image.
Cheers
Rob