I have successfully installed the SCT and FSLeyes. Now, I am trying to run FSLeyes. In order to do that I write the command: fsleyes &
Commands and terminal output
Failed to load plugin file /home/ali/.config/fsleyes/plugins/sct_plugin.py: name 'frame' is not defined.
But afew seconds later the FSLeyes window normally opens up. There, when I want to import SCT plugin by clicking the “run script”, it shows this error message:
The script /home/ali/sct/contrib/fsl_integration/sct_plugin.py has crashed! Reason: ‘FSLeyesFrame’ object has no attribute ‘getAuiManager’
path: /home/ali/sct
OS: linux (Linux-5.8.0-55-generic-x86_64-with-debian-bullseye-sid)
CPU cores: Available: 4, Used by ITK functions: 4
RAM: Total: 5828MB, Used: 1894MB, Available: 3149MB
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/ali/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] (1.4.1)
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] (6.2.4)
Check if pytest-cov is installed…[OK] (2.12.1)
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] (0.24.2)
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] (4.61.0)
Check if transforms3d is installed…[OK] (0.3.1)
Check if urllib3 is installed…[OK] (1.26.5)
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…QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to ‘/tmp/runtime-root’
[OK]
Just to clarify, sct_plugin.py shouldn’t be copied to the plugins directory. Instead, it should be left in the SCT directory, then opened using “Run script”.
Thank you so much. I used the FSL method.
When I try to open it by using “run script” from inside the FSLeyes screen, It shows this error message:
The script /home/ali/sct/contrib/fsl_integration/sct_plugin.py has crashed! Reason: ‘FSLeyesFrame’ object has no attribute ‘getAuiManager’
Thank you very much. When I type the “fsleyes --version”, it shows:
Failed to load plugin file /home/ali/.config/fsleyes/plugins/sct_plugin.py: name ‘frame’ is not defined.
And when I type “find $FSLDIR -name ‘wxpython-*’ -type d 2>/dev/null”, it shows:
/usr/local/fsl/fslpython/pkgs/wxpython-4.0.7.post2-py37h17634e0_3
This error occurs because you have placed “sct_plugin.py” in the “plugins/” folder. Instead, “sct_plugin.py” should stay in its original location (the SCT installation folder).
Please remove “sct_plugin.py” from the “plugins/” directory, then rerun “fsleyes --version”.
I removed the sct_plugin.py from the plugins folder. Now, when I run the “fsleyes --version” command, the previous error message has been disappeared. But I don’t have any clue why it still shows the same error message when I click the “run script” from inside the FSLeyes window.
I re-installed the FSLeyes but didn’t work. I also tried installing FSLeyes through the Conda method but it didn’t work either.
I am happy to help try and debug. But, the reason we ask for the output of “fsleyes --version” is because the version number helps us to try to reproduce your issue.
Thank you for the information. I have been able to reproduce your issue, and I can confirm that this is a bug specifically related to FSLeyes v1.0. (We have tested the “sct_plugin.py” script against FSLeyes version 0.34, but not the recently-released v1.0.)
An issue has been opened in our issue tracker here. I will get to work shortly to address this issue, then I will update you when a fix has been released.
