Mrtrix3 for NITRC HCP Computing Environment

Dear experts,

I’m working with HCP data in the The NITRC Human Connectome Project Computing Environment with AWS.
mrtrix3 is already there but there are a lot of problem running the script (e.g. 5ttgen etc.). Moreover a lot of programs are not include in the installation such as tckgen etc.)

So I decided to install mrtrix3 again following the Standalone installation on Linux at the following link:

So I’ve run the command

./build clean
git pull
./configure -static [-nogui]

but the processing is kind of stuck at this step:

(179/505) [CC] tmp/src/registration/transform/initialiser_helpers.o

Do you have any suggestions

thanks a lot


Have you checked whether your system has run out of RAM and is using swap? Compiling the registration code is quite memory thirsty.

Dear Max,

I’ve run


but the things didn’t change

Do you have any tips?



Static build isn’t something I do often, so I’m not sure where the problem is. On top of that, I don’t expect many developers in general to be using static builds, it’s quite a rare requirement. There’s a good chance this might be a compiler bug…

What system are you running this on? It might be that the simplest is just to try on a different system running a different version or distribution of Linux – maybe in a VM or container…

I can not reproduce this with the latest master using clang 3.8.0 (ubuntu 16.04).

My -static -nogui build completes in 372 steps. I only get 505 steps if I configure without these flags.

That’s purely down to the -nogui flag, which skips compilation of any GUI-related source file. Davide seemed to suggest that his static build hangs on that file whether -nogui was specified or not, but presumably we were looking at the output of the ./configure -static run…