Improve README

[NathanMolinier]

Description

It looks like some information are missing in the README and it is not that intuitive to use the module:

• How to open the extension ? (Don't understand step 7.) -- people need to know that they need to click on the dropdown menu for version 5.7.0:

• Should we create a python environment ? Which python version ?

• How to download Slicer 5.2.2. -- 3D Slicer version 5.2.2 link #61

• The videos are a bit old and the UI has changed since

[sandrinebedard]

How to find the config file:

[NathanMolinier]

I'm not able to find the "examples" section in the drop down menu after adding the path and allowing developper mode:

slicer version 5.2.2

[valosekj]

It's not clear to me what "Window Level" and "Window Width" stand for

[tomDag25]

It seems you can automate the window level and window width in the Module section using Automatic W/L. It would be great to make it a default parameter and if you want to change the W/L you can but not force the user to put some arbitrary values.

[AcastaPaloma]

@NathanMolinier did you add the src folder specifically - into the modules section? I think you have to put the direct parent folder of the python file for the extension.

@sandrinebedard You should be able to create a new segmentation and create an output folder from there. Only then you should be able to pick up from an existing output folder for segmentation/classification settings, labels, etc.

[NathanMolinier]

Yes I did it, see my screenshot:

I found this but I don't know how to load the module

Update: I managed to solve the problem by recloning the repository and installing missing python packages. It's not really clear why I had this issue in the first place.

[maxradx]

• #Add tree in folder organization to specify how it shouldbe organized.

[maxradx]

Work in progress related to updating documentation. Will notify when up-to-date!

[maxradx]

issue 62

@NathanMolinier
Should we create a python environment ? Which python version ? --- Slicer install its own version of Python, which is not the traditionnal version (mixed up with C++). If Slicer is able to be opened, then no need for other version of Python.
The videos are a bit old and the UI has changed since --- Only one up-to-date video (As of 2024-11-18) has been kept in the documentation PR.
I'm not able to find the "examples" section in the drop down menu after adding the path and allowing developper mode: --- that means SlicerCART has not been installed correctly. Try using the updated Installation steps (e.g. dragging the SlicerCART.py file in the module window although only the path appears)

@sandrinebedard
How to find the config file: --- you are right. This has to be implemented (not working with the actual version) only use-case scenario for now is

@valosekj
It's not clear to me what "Window Level" and "Window Width" stand for --- those are scans-related values. Should be disabled in MRI is not selected as the modality. There are issues related to it, that will be fixed in further PR.

@tomDag25
It seems you can automate the window level and window width in the Module section using Automatic W/L. It would be great to make it a default parameter and if you want to change the W/L you can but not force the user to put some arbitrary values. --- sure. Please refer to #67

All of this are addressed in the Pull Request 105 (#105) related to Documentation.

In brief, those aspects are addressed in PR 105. Please refer to it for any discussion.

Thanks.