I installed mrtrix3 on windows 10 enterprise via mingw64 as per instructions. I can run mrtrix3 from the mingw64 shell/command line just fine (not from the system/win command prompt). I wanted to run mrtrix3 commands from matlab via system command, but I do not seem to be able to.
In matlab, I tried smth like
cmd = 'C:\msys64\mingw64.exe; cd C:/msys64/home/user/mrtrix3/bin; command1 ; command2 etc '; [a b]=system (cmd);
but it does not work.
I would like to open an interactive shell with output/progress visible in the command window, or otherwise showing in matlab.
Please advise; my $path in mingw64 is
$ echo $PATH /home/user/mrtrix3/bin:/mingw64/bin:/usr/local/bin:/usr/bin:/bin:/c/Windows/System32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl
Unrelated, the main reason to run mrtrix on my windows box is slow tcksift run on my linux box. From previous threads, there is no config file generated on Win installations due to compilation from source. If one wants to view the default -nthreads setting with the tcksift command in order to keep it or up it, how to go about it? More generally, how to view/change config options in windows mrtrix?