HI @jbcmarsman,
This may come too late to be of any use to you, but just in case:
If you have manually set your PATH to include $FSLDIR/bin, this will cause all kinds of issues – see e.g. this post for some details into the issue. You can check by typing:
echo $PATH
Basically, the FSL team recommends your FSL setup should be done by setting $FSLDIR and invoking the $FSLDIR/etc/fslconf/fsl.sh script – which will take care of setting up the PATH appropriately. You may find all it takes for MRtrix to compile properly is to rectify this…
All the best,
Donald