Installation and Running

Hi,

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 “mrview” nothing pops up. Would love assistance to get this working. Thanks!!

1 Like

Hi @Hunainabri,

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 I’ve not see before:

warning: database file for 'clangarm64' does not exist (use '-Sy' to download)

I can’t find much information about what this means, but it looks suspiciously like you might be running on an ARM64 system…? 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 doesn’t work…

All the best,
Donald.

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?

Thanks!
Hunain

OK, so that’s not the issue…

To check whether you’re running in the right terminal, I think the simplest things is to type:

echo $MSYSTEM

Also, I’m not sure whether you’re getting a ‘command not found’ 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 it’ll work on yours too…).

If you are getting ‘command not found’ errors, what does “which mrview” report? And what is the output of “echo $PATH”?

It’s 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 hang…?

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!

Hunain

Hi @Hunainabri,

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 isn’t working, then the issue isn’t related to the GUI aspects. I’ve 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 I’d expect. I have no idea what the issue could be…

Has anyone else on this forum encountered this issue?

All the best,
Donald.

A post was split to a new topic: MRtrix3 on anaconda

Hi,

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.

Best regards,
Stefan

Ok, thanks for the report. I’ll investigate when I have a minute – it’s hopefully something simple… :crossed_fingers:

FYI. Building mrtrix from the sources worked fine. So I guess that might be a workaround for @Hunainabri as well…

1 Like

Thanks! I will try that. could you further explain what you mean by sources? I am very new to this and still trying to get it to work :sweat_smile:

Hunain

Just follow these instructions: Building MRtrix3 from source

I have been following that and I am met with this after downloading the necessary dependencies and cloning the git.

I am not very tech savvy with this type of stuff so i am not sure where to go from here. I appreciate the guidance

I’m having the same behaviour. it seems to have installed like it should, but nothing happens.

$ which mrview
/mingw64/bin/mrview

jriph@JMR-Precision-7550 MINGW64 ~
$ mrinfo
(nothing)

jriph@JMR-Precision-7550 MINGW64 ~
$ which mrinfo
/mingw64/bin/mrinfo

OK, I’ve had a look into it, did a full clean install, and the same thing happens to me too. I’ll investigate and see if I can work out what the problem is…

OK, I think I’ve 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.

I’ve 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:

pkg=$(curl -s https://api.github.com/repos/MRtrix3/mrtrix3/releases/latest | grep browser_download_url.*.tar.zst | awk '{print $2}' | tr '"' ' ' | sort -n | tail -n 1 )
echo $pkg
curl -L $pkg -O
pacman -U $(basename $pkg)

Let me know if it works!

Cheers,
Donald.

It Worked! Thanks a bunch I appreciate all the help.

  • Hunain
1 Like

Seems to work ! :pizza:

1 Like