Installing SCT on Ubuntu 20.04

Hi,
I am trying to install SCT on Ubuntu 20.04. I am getting following error message

Check if urllib3 is installed…[OK] (1.26.4)
Check if pytest_console_scripts is installed…[OK]
Check if wquantiles is installed…[OK] (0.4)
Check if spinalcordtoolbox is installed…[OK]
Check ANTs compatibility with OS …[OK]
Check PropSeg compatibility with OS …[OK]
Check if DISPLAY variable is set…[OK]
Check if figure can be opened with PyQt…MoTTY X11 proxy: Authorisation not recognised

In case you are trying to start a graphical application with “sudo”, read this article in order to avoid this issue:

qt.qpa.screen: QXcbConnection: Could not connect to display localhost:10.0
Could not connect to any X display.

Installation validation Failed!

Installation failed!

Please copy the output of this Terminal (starting with the command install_sct) and upload it as a .txt attachment in a new topic on SCT’s forum:

–> http://forum.spinalcordmri.org/c/sct

I have tried to add xauth to the Linux user but its still giving me same error.

Hi @hussnain,

It is worth noting that the only part of the installation that failed was the check to see if PyQt GUI windows can be opened. But, only a small part of SCT uses PyQt, so you should be able to run most of the functionality in SCT without any issues. :slight_smile:

If you would like to still debug the display issues, though, I would be happy to help!

I have a few questions:

  • When you installed SCT, did you run “./install_sct” or “sudo ./install_sct”?
  • Could you please run the command “sct_check_dependencies” in your terminal, and paste the entire output?

Kind regards,
Joshua

@joshuacwnewton Thanks for replying

  1. Command used ./install_sct
  2. Output.
    sct_check_dependencies


Spinal Cord Toolbox (git-HEAD-e2e19bd02e2a99eab252ad3cca86eee5c5d63e92)

sct_check_dependencies

SCT info:

  • version: git-HEAD-e2e19bd02e2a99eab252ad3cca86eee5c5d63e92
  • path: /home/hussnain.tariq/sct
    OS: linux (Linux-5.4.0-74-generic-x86_64-with-debian-bullseye-sid)
    CPU cores: Available: 2, Used by ITK functions: 2
    RAM: Total: 3936MB, Used: 222MB, Available: 3421MB
    Check Python executable…[OK]
    Using bundled python 3.6.13 |Anaconda, Inc.| (default, Jun 4 2021, 14:25:59)
    [GCC 7.5.0] at /home/hussnain.tariq/sct/python/envs/venv_sct/bin/python
    Check if data are installed…[OK]
    Check if colored is installed…[OK] (1.4.2)
    Check if dipy is installed…[OK] (1.4.0)
    Check if futures is installed…[OK]
    Check if h5py is installed…[OK] (2.10.0)
    Check if Keras (2.1.5) is installed…[OK] (2.1.5)
    Check if ivadomed is installed…[OK] (2.7.4)
    Check if matplotlib is installed…[OK] (3.3.4)
    Check if nibabel is installed…[OK] (3.2.1)
    Check if numpy is installed…[OK] (1.19.5)
    Check if onnxruntime (1.4.0) is installed…[OK] (1.4.0)
    Check if pandas is installed…[OK] (1.1.5)
    Check if psutil is installed…[OK] (5.8.0)
    Check if pyqt5 (5.11.3) is installed…[OK] (5.11.3)
    Check if pytest is installed…[OK] (6.2.3)
    Check if pytest-cov is installed…[OK] (version = ‘2.11.1’)
    Check if raven is installed…[OK]
    Check if requests is installed…[OK] (2.25.1)
    Check if requirements-parser is installed…[OK] (0.2.0)
    Check if scipy is installed…[OK] (1.5.4)
    Check if scikit-image is installed…[OK] (0.17.2)
    Check if scikit-learn is installed…[OK] (0.24.1)
    Check if tensorflow (1.5.0) is installed…[OK] (1.5.0)
    Check if torch (1.5.0+cpu) is installed…[OK] (1.5.0+cpu)
    Check if torchvision (0.6.0+cpu) is installed…[OK] (0.6.0+cpu)
    Check if xlwt is installed…[OK] (1.3.0)
    Check if tqdm is installed…[OK] (4.60.0)
    Check if transforms3d is installed…[OK] (0.3.1)
    Check if urllib3 is installed…[OK] (1.26.4)
    Check if pytest_console_scripts is installed…[OK]
    Check if wquantiles is installed…[OK] (0.4)
    Check if spinalcordtoolbox is installed…[OK]
    Check ANTs compatibility with OS …[OK]
    Check PropSeg compatibility with OS …[OK]
    Check if DISPLAY variable is set…[OK]
    Check if figure can be opened with PyQt…MoTTY X11 proxy: Authorisation not recognised

In case you are trying to start a graphical application with “sudo”, read this article in order to avoid this issue:

qt.qpa.screen: QXcbConnection: Could not connect to display localhost:10.0
Could not connect to any X display.

Thank you for the reply!

I believe you are connecting to the Ubuntu computer using MobaXterm from a Windows computer, right?

If so, it looks like the error is related to X11 forwarding. I’d like to double-check that you are able to display GUI applications other than SCT. Could you please follow these steps and verify whether the xclock command shows a pop-up with a clock?

Kind regards,
Joshua

Josh you are right, I am already investigating This part I was unable to open any GUI based
app.

1 Like

Dear @hussnain,

Just to check, were you able to resolve your GUI issue with SCT?

Kind regards,
Joshua