Add SlicerTractParcellation extension

[zhangfanmark]

New extension

• Repository name is Slicer+ExtensionName (except if the repository that hosts the extension can be also used without Slicer)
• 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 and the name of the license is mentioned in extension homepage. 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. MIT (https://choosealicense.com/licenses/mit/) or Apache (https://choosealicense.com/licenses/apache-2.0/) license is recommended. Read here to learn more about licenses. If source code license is more restrictive for users than MIT, BSD, Apache, or 3D Slicer license then describe the reason for the license choice and include the name of the used license 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
• Content of submitted json file is consistent with the top-level CMakeLists.txt file in the repository (dependencies, etc. are the same)
• 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
  • Publication: link to publication and/or to PubMed reference (if available)
• Hide unused github features (such as Wiki, Projects, and Discussions, Releases, Packages) 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)
• The extension is safe:
  • Does not include or download binaries from unreliable sources
  • Does not send any information anywhere without user consent (explicit opt-in is required)

[pieper]

@zhangfanmark thanks for putting this together. Please do go through the checklist in this template and perform the steps. It may seem like a lot but they should be quick for either you or Kening to do. Things like including some screenshots and descriptive text to form a tutorial will really help anyone who wants to use your tutorial. Also adding the 3d-slicer-extension will make it easier for people to find. Plus it will show off your work!

[zhangfanmark]

Hi @pieper Kening is working on the checklist and he will do a pull request later. Thank you!!!

[pieper]

Thanks Fan 👍 If Kening has any questions at all, let us know.

[JoshuaKening]

@pieper We have accomplished the extension, https://github.com/SlicerDMRI/SlicerTractParcellation, here is the link. Please let me know if there are any imperfections. And do we need to create a new pull request to refresh the version?

[pieper]

Hi Kening - The license is good and the image looks nice so thanks for the update.

What we were looking for is the items on the checklist at the top of this page, e.g. going through point by point and ensuring that the listed items have been taken into account.

For example, the first unchecked box is "Extension description summarizes in 1-2 sentences what the extension is usable (should be understandable for non-experts)". While there is a sentence in the README, I'm not sure it's appropriate yet, since very few people would know what WMA or ORG are. Here it would be nicer to spell out the terms "White Matter Analysis" and "O'Donnell Research Group" and include links to places where they can get more information.

Another point is that the URLs in the CMakeLists file haven't been updates. For example, this line still has the placeholder example.com in the path, which is clearly not the path to the screenshots.

You can have a look at other extensions to see how they have addressed the checklist items. Here's a recent example that is nicely done: SlicerMONAIAuto3DSeg. It has a nice description and several images that give a clear idea what the extension does. It also has valid URLs and other content.

You don't need a new pull request, just update your site and edit the checklist above as you confirm that each of the topics has been addressed.

I hope it's clear why we ask developers to follow this template so that users can discover and understand your contributions.

Best,
Steve

@JoshuaKening @zhangfanmark @ljod

[lassoan]

@pieper do you think we can accept this extension as Tier 1 (due to lack of documentation)

[pieper]

I guess I'd hold off until we hear more from @zhangfanmark or @JoshuaKening -- if there's continued development then yes it's good to have a working extension for user testing, but if the project isn't going forward and it's not quite usable now it might be better to have it in an archive in case someone is able to pick it up in the future. @ljod do you know the status?

[zhangfanmark]

Hi @pieper sorry that this was suspended. Kening has just picked it up and updated the repo for the checklist. The changes have been merged into SlicerTractParcellation. Can you please take a look and see if it is okay now? Thank you!!!

@ljod @JoshuaKening

[pieper]

Thanks @zhangfanmark 👍

@lassoan do you want to make this tier 1 or 3? I'm fine either way.

[lassoan]

It has some documentation/tutorial now, so tier 3 should be appropriate.