Hi Saman,
Problem #1:
OSError: [Errno 2] No such file or directory: '/usr/local/bin/src/dwi2response'
suggests that you have manually moved the dwi2response script into /usr/local/bin/. This won’t work: The bulk of the dwi2response code resides in <mrtrix3_dir>/scripts/src/dwi2response/, and is dynamically queried & run whenever dwi2response is run. This keeps the code for different algorithms separate from one another, and you can even write your own response function estimation algorithm and it will automatically become available as an option in dwi2response (your algorithm’s options will even appear in the help page!). But because this directory can’t be found based on a relative path from dwi2response itself, the script crashes out (I’ll add a more elegant error message). You’re better off adding <mrtrix3_dir>/scripts/ to your PATH environment variable.
The second screenshot doesn’t give us enough information to know what is wrong; the better solution is to capture the entire text output and copy&paste here, wrapped in between triple back-ticks like this for better readability:
```
sh-3.2# ./build
( 1/427) release/cmd/dwi2mask.o
( 2/427) ...
```
On the off chance that you updated MRtrix3 from a pre-March installation, there may be additional steps needed; e.g. you can try re-running the configure script prior to the build script.
Cheers
Rob