Add SlicerDBSCoalignment extension

[IVarha]

Adding DBS Coalignment project to coalign MER signals within STN for PD surgeries

---

New extension

Tier 1

Any extension that is listed in the Extensions Catalog must fulfill these requirements.

• 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)

[IVarha]

Hello, This module is designed to Coalign electrodes and refine their positions in DBS surgeries.
Is there any problems with it?

[pieper]

Hi - thanks for the contribution and the ping. I know people are busy and haven't had time to review. I took a quick look and I think this looks good for a Tier 1 module. We are trying to use the tier 1 process to unclog the review process but since you can also install without the extension manager feel free to publicize your work and then just change the readme when it gets reviewed.

One suggestion on the readme is to describe a bit more context of the kind of experiments this would be used for (I assume it's for mice, right?).

[IVarha]

Dear Steve,

Thank you for your reply. I was curious whether I submitted correctly.
Our package was tested on data from the hospital of Homolka on human PD patients who underwent DBS surgeries, and could be tested on example from the LeadOR package (from SlicerNetsim).
I made our package dependent on a SlicerNetsim as I am primarily extending on top of it.
Thank for the suggestion, I will definitely update the readme (as paper is still in consideration and when I will receive doi, there will be reference to a paper, and figures from it).

Thanks Igor

[lassoan]

The automatic validation checks have some issues. Could you fix them?
https://github.com/Slicer/ExtensionsIndex/actions/runs/17519949374

If you have any questions then let us know.

[lassoan]

Thanks for the update! A few checks are still failing:

❌ Check CMakeLists.txt content failed: CMakeLists.txt file not found in repository root

Fix: move https://github.com/IVarha/SlicerDBSCoalignment/tree/master/slicer_mer_stn folder content to the repository root folder

❌ Check category failed: Category Netsim is unknown. Consider using any of the known extensions instead: Active Learning, Analysis, Auto3dgm, BigImage, Cardiac, Chest Imaging Platform, Conda, Converters, DICOM, DSCI, Developer Tools, Diffusion, Examples, Exporter, FTV Segmentation, Filtering, Filtering.Morphology, Filtering.Vesselness, Holographic Display, IGT, Informatics, Netstim, Neuroimaging, Nuclear Medicine, Orthodontics, Osteotomy Planning, Otolaryngology, Photogrammetry, Pipelines, Planning, Printing, Quantification, Radiotherapy, Registration, Remote, Rendering, SPHARM, Segmentation, Sequences, Shape Analysis, Shape Regression, Shape Visualization, Simulation, SlicerCMF, SlicerMorph, Spectral Imaging, Supervisely, Surface Models, SurfaceLearner, Tomographic Reconstruction, Tracking, Tractography, Training, Ultrasound, Utilities, Vascular Modeling Toolkit, Virtual Reality, VisSimTools, Web System Tools, Wizards

Fix: fix typo (Netsim -> Netstim)

[IVarha]

Dear Andras,
Thank you seems to me issue is already fixed.
I edited the main project as well as file in pull request

[lassoan]

Thank you, it all looks good now.

In the long term, it would be nice to replace the tensorflow dependency with pytorch so that users can simply install the Slicer extension without messing with additional Python environments, but I understand that this may not be easy.