Ok, it looks like you’ve got anaconda installed, and that’s the likely problem. We’ve removed it from the path, since it’s actually really difficult to use anaconda for this, so it’s best avoided. But in your case, you’ve probably still got the CXX and/or LD variables set to point to the anaconda versions – which are no longer in the path…
To get this working, you’ll need to use the XCode compiler. Assuming you have it installed, try unsetting the variables I mentioned before issuing ./configure:
unset CXX
unset LD
./configure
Hopefully that’ll fix it…
On that note, we are planning on providing precompiled versions of MRtrix3 for installation via anaconda. Hopefully within the next few weeks…