I am new to MRTrix3 and ran the Download and Installation instructions online. I redownloaded using the code form the instruction and was met with this:
$ pkg=$(curl -s https://api.github.com/repos/MRtrix3/mrtrix3/releases/latest | grep browser_download_url.*.tar.xz | awk '{print $2}' | tr '"' ' ' | sort -n | tail -n 1 )
echo $pkg
curl -L $pkg -O
pacman -U $(basename $pkg)
https://github.com/MRtrix3/mrtrix3/releases/download/3.0.4/mingw-w64-x86_64-mrtrix3-3.0.4-1-x86_64.pkg.tar.xz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 8395k 100 8395k 0 0 483k 0 0:00:17 0:00:17 --:--:-- 444k
warning: database file for 'clangarm64' does not exist (use '-Sy' to download)
loading packages...
warning: mingw-w64-x86_64-mrtrix3-3.0.4-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...
Packages (1) mingw-w64-x86_64-mrtrix3-3.0.4-1
Total Installed Size: 51.02 MiB
Net Upgrade Size: 0.00 MiB
:: Proceed with installation? [Y/n] y
(1/1) checking keys in keyring [#########################################] 100%
(1/1) checking package integrity [#########################################] 100%
(1/1) loading package files [#########################################] 100%
(1/1) checking for file conflicts [#########################################] 100%
(1/1) checking available disk space [#########################################] 100%
:: Processing package changes...
(1/1) reinstalling mingw-w64-x86_64-mrtrix3 [#########################################] 100%
Therefore, I believe it installed correctly. Then when I type āmrviewā nothing pops up. Would love assistance to get this working. Thanks!!
Can you provide more detail on your system and OS? Is this on Windows 10 or 11? Using the latest version of MSYS2? Run from the MinGW64 terminal? Using what hardware exactly?
There is also an odd error message that Iāve not see before:
warning: database file for 'clangarm64' does not exist (use '-Sy' to download)
I canāt find much information about what this means, but it looks suspiciously like you might be running on an ARM64 systemā¦? I have heard that Microsoft were trying to provide builds of Windows for ARM processors, is this what you have? If so, that would explain why this doesnāt workā¦
I am on Windows 10 using a x64-based processor. I believe I am using the latest MSYS2 and MinGW64 terminal as I followed the download instructions from MRTrix3 and MSYS webpage. How would I about checking that?
To check whether youāre running in the right terminal, I think the simplest things is to type:
echo $MSYSTEM
Also, Iām not sure whether youāre getting a ācommand not foundā error, or just that mrview seems to hang. If you type mrinfo, do you see the help page for that command? If that works, what happens if you type mrview -help? If that also shows the help page for mrview, then the issue might be related specifically to the graphics. You could try starting mrview with the -debug option and see if that shows anything interesting in the terminal (Windows makes it difficult for GUI applications to interact with the terminal, but this seems to work on my Windows 11 system, so hopefully itāll work on yours tooā¦).
If you are getting ācommand not foundā errors, what does āwhich mrviewā report? And what is the output of āecho $PATHā?
Itās worth bearing in mind that for some reason Qt (GUI) applications can take some time to start up the first time on MSYS2, so it could be just a matter a waiting a bit longer if it seems to hangā¦?
Here is a screenshot of everything you recommended to try. I have left the terminal open for hours after entering mrview, etc. and still nothing pops up. what would you recommend for the next steps? I also appreciate all the help!
Just to confirm: typing mrinfo shows nothing at all? You should see the command help page, which you can navigate through and exit by typing q.
If even that isnāt working, then the issue isnāt related to the GUI aspects. Iāve not come across anything like that before, my best guess at this point is that there is interference from some kind of antivirus protection or something of that nature. Are you running anything like that?
Otherwise, everything seems to be set up as Iād expect. I have no idea what the issue could beā¦
Has anyone else on this forum encountered this issue?
After moving to a new freshly installed computer over the past days (Windows10.0.19044, x64 i7) I saw exactly the same behaviour after installing msys and mrtrix. No output at all for any mrtrix command. During the installation there was also the warning about the missing clangarm64. Apparently it was installed in the further process of the installation as a later call to pacman -Sy showed that no update on clangarm64 was required.
OK, Iāve had a look into it, did a full clean install, and the same thing happens to me too. Iāll investigate and see if I can work out what the problem isā¦
OK, I think Iāve got it working again. As far as I can tell, this was due to a change in the name of the libtiff-5.so library in the libtiff package shipped by MSYS2, which prevented the executables from running.
Iāve recompiled a fresh version of MRtrix, which should now use the version currently found on an up to date MSYS2 install, and replaced the previous MSYS2 package on the releases page with this updated one.
Long story short: please run the installation instructions again (copied below for convenience), as per the MRtrix3 MSYS2 download page:
