Add SlicerBrats extension

[saimasafdar2021]

I have created one extension and have added all the scripted CLI extensions. SlicerBratsPreprocessor
SlicerBratsSegmentator
SlicerBratsFusionator
Also I have added the scripted module
BatchBrainMRTumorSegmentation which is calling the above cli modules to perform preprocessing, segmentation and lastly fusion.

New extension

• Extension has a reasonable name (not too general, not too narrow, suggests what the extension is for)
• Repository name is Slicer+ExtensionName
• Repository is associated with 3d-slicer-extension GitHub topic so that it is listed here. To edit topics, click the settings icon in the right side of "About" section header and enter 3d-slicer-extension in "Topics" and click "Save changes". To learn more about topics, read https://help.github.com/en/articles/about-topics
• Extension description summarizes in 1-2 sentences what the extension is usable (should be understandable for non-experts)
• Any known related patents must be mentioned in the extension description.
• LICENSE.txt is present in the repository root. MIT (https://choosealicense.com/licenses/mit/) or Apache (https://choosealicense.com/licenses/apache-2.0/) license is recommended. If source code license is more restrictive for users than MIT, BSD, Apache, or 3D Slicer license then the name of the used license must be mentioned in the extension description.
• Extension URL and revision (scmurl, scmrevision) is correct, consider using a branch name (main, release, ...) instead of a specific git hash to avoid re-submitting pull request whenever the extension is updated
• Extension icon URL is correct (do not use the icon's webpage but the raw data download URL that you get from the download button - it should look something like this: https://raw.githubusercontent.com/user/repo/main/SomeIcon.png)
• Screenshot URLs (screenshoturls) are correct, contains at least one
• Homepage URL points to valid webpage containing the following:
  • Extension name
  • Short description: 1-2 sentences, which summarizes what the extension is usable for
  • At least one nice, informative image, that illustrates what the extension can do. It may be a screenshot.
  • Description of contained modules: at one sentence for each module
  • Tutorial: step-by-step description of at least the most typical use case, include a few screenshots, provide download links to sample input data set
  • Publication: link to publication and/or to PubMed reference (if available)
  • License: We suggest you use a permissive license that includes patent and contribution clauses. This will help protect developers and ensure the code remains freely available. We suggest you use the Slicer License or the Apache 2.0. Always mention in your README file the license you have chosen. If you choose a different license, explain why to the extension maintainers. Depending on the license we may not be able to host your work. Read here to learn more about licenses.
  • Content of submitted json file is consistent with the top-level CMakeLists.txt file in the repository (dependencies, etc. are the same)
• Hide unused features in the repository to reduce noise/irrelevant information:
  • Click Settings and in repository settings uncheck Wiki, Projects, and Discussions (if they are currently not used)
  • Click the settings icon next to About in the top-right corner of the repository main page and uncheck Releases and Packages (if they are currently not used)

[jcfr]

Related issues:

• Ensure bratsFusionator/bratsPreprocessor/bratsSegmentor are distributed UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation#2

[saimasafdar2021]

Hi JCFR,
Any update on this extension please?

regards,
Saima

[jcfr]

re: Any update on this extension please?

Since force pushing the topic does not seem possible. Could you rebase and update it ? 🚀

Thanks for your patience 🙏

[saimasafdar2021]

Hi JCFR,
Could you please let me know what can I do to get this extension published? What is the problem?
what does it mean rebase and update? should I do it at my end.

regards,
Saima

[bmcmoolpaad]

I traced the publication blockers and prepared a clean replacement path:

• BatchBrainMRTumorSegmentation #2008 was closed without merge, so it was never eligible to appear in Extension Manager.
• This PR currently adds SlicerBrats.json, but its scm_url (https://github.com/UWA-Medical-Physics/SlicerBrats.git) returns 404. The last validate-extensions and ai-analysis checks therefore failed.
• The original source repository also did not distribute the three helper scripts in its package, as tracked in Ensure bratsFusionator/bratsPreprocessor/bratsSegmentor are distributed UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation#2.

I submitted UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation#3 to package the helpers as scripted CLI modules and correct the metadata/documentation. I also opened draft replacement #2384 with a catalog filename that matches the source CMake project. The current Extension Index validator passes against the repaired source branch.

After source PR #3 is merged and the official source repository is given the 3d-slicer-extension topic, #2384 can be switched to the official main branch and marked ready. This PR can then be closed as superseded.