fsleyes: allow user to specify output folder

[Drulex]

Closes #2579

Implement: #2579 (comment)

[Drulex]

Do you mind giving the updated GUI a try @valosekj ?

[valosekj]

Do you mind giving the updated GUI a try @valosekj ?

Sure! But now I am somehow struggling with running the sct_plugin.py script from fsleyes. I start fsleyes from terminal, then i do File/Run script and then I get invalid syntax error on line 110:

https://github.com/neuropoly/spinalcordtoolbox/blob/bacf0325eaafa71e3f6cfa4be83f0996c903dd3b/contrib/fsl_integration/sct_plugin.py#L110

It is probably related to f-strings formatting. This formatting is available from Python3.6, right? Is it possible that my fsleyes tries to run the sct_plugin.py by older version of python?
How do you run fsleyes and the plugin? Thanks!

[jcohenadad]

@valosekj i just tried and it works fine. What version/os are you on? Me:

• OS: macOs 10.15.7
• fsleyes/FSLeyes version 0.31.0+build0

[valosekj]

macOS Catalina 10.15.7
fsleyes/FSLeyes version 0.27.3+build0

I am going to update FSLeyes and I will see.

[Drulex]

It is probably related to f-strings formatting. This formatting is available from Python3.6, right?

Yes it is a feature from 3.6. Considering that the python version we bundle with install_sct is 3.6 I assumed it was ok.

[valosekj]

I have updated FSLeyes to 0.34.2 and now I am able to run sct_plugin.py but when I click on Run button e.g. for sct_propseg I get:

Probably some other problem with my environment. I will try to figure out what is reason.

[Drulex]

Probably some other problem with my environment. I will try to figure out what is reason.

I was running 0.33, but I upgraded to 0.34.2 and confirm that the feature still works as expected (python 3.8.5 on Linux 5.4)

[Drulex]

@valosekj I think if you run fsleyes from the conda environment it will pickup the 3.6 version.

source $SCT_DIR/python/etc/profile.d/conda.sh && conda activate venv_sct && fsleyes

[valosekj]

@valosekj I think if you run fsleyes from the conda environment it will pickup the 3.6 version.

source $SCT_DIR/python/etc/profile.d/conda.sh && conda activate venv_sct && fsleyes

I was running fsleyes in conda environment in #2941 (comment). Strange. It will be probably something related to MacOS Catalina - https://stackoverflow.com/a/59150657. I am digging into it.

[Drulex]

I was running fsleyes in conda environment in #2941 (comment). Strange. It will be probably something related to MacOS Catalina - https://stackoverflow.com/a/59150657. I am digging into it.

Ah ok. That's a weird one.. good luck. 😬

[Drulex]

Any luck @valosekj ?

[valosekj]

Any luck @valosekj ?

Unfortunatelly not. But I think, PR can me merger, because it is working for you and also for Julien who has MacOS. It looks that my issue is probably caused by some problem related to my computer and SW versions.

[Drulex]

Unfortunatelly not. But I think, PR can me merger, because it is working for you and also for Julien who has MacOS. It looks that my issue is probably caused by some problem related to my computer and SW versions.

@jcohenadad ok with the changes to be merged?