Error after updating to the latest version (Windows MSYS2)


Firstly, thank you for this wonderful software!

I have been using it for a while and just updated to version 3.0 RC1.

But, I have some issues running any command.

Looking forward to your comments!


Wow, I haven’t seen anything like this before… Can I just check whether you’ve had any issues with this particular data set before? I’m surprised that the progress bar (the percentage indicator) would show something like this, it would seem to indicate that there is no data in the image or something? What does mrinfo dwi.mif report?

Hi Jacques-Donald,

No, I had no problems previously with this dataset (MRtrix ver 0.3.16). mrinfo seems to work fine

Just to clarify, I am working on a rat data set acquired at 0.150 mm isotropic upsampled by a factor of 2.

Can you do a ./build clean, make sure the release/ directory is no longer present in the main MRtrix3 directory, then re-run ./build? It shouldn’t be possible for old and new object files / shared libraries to get mixed up, and even if they did you should get a “symbol not found” error; but I’ve seen MSYS do some weird things…

Also, can you post the full contents of the file config (in the root MRtrix3 directory)? Just in case there’s anything weird in there.

Hi Rob,

A clean rebuild did the trick!