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:
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.
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?
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.
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?
