ENH: Add PKDIA extension

[Jo-Byr]

New extension

Tier 1

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Tier 3

Community-supported extensions.

• Extension has a reasonable name (not too general, not too narrow, suggests what the extension is for)
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• All requirements of tiers < 5.

[finetjul]

@lassoan @jcfr is there something we forgot in the procedure to get the extension reviewed/merged ?

[lassoan]

Sorry for the delay, holidays and the Project Week made a the last couple of weeks very busy. I have a couple of comments, I'll post them by Monday.

[lassoan]

Thank you for your contribution @Jo-Byr et al, very nice work! There are just a few things that would need to be considered before merging the pull request, just because it would be difficult to change it later, and a few more to make the module more successful and impactful.

Before merge:

• Extension name: It is good that it is short and quite specific, but most people would have no idea what PKDIA stands for and it is hard to remember. Many users would not discover it or could not find it or would not recommend it because they don't remember the exact letter combination. It is also unfortunate that the google hits for PKDIA are in the medical domain but something completely different. Including "kidney" and "segmentation" in the name would help a lot. You could consider names like KidneySegPKDIA or PKDIAKidneySeg or maybe PolycysticKidneySeg. Or, if you are ready to add or accept other kidney segmentation modules into this extension in the future then it could be just KidneySeg.
• Module name: In general, we avoid starting each module name with "Slicer", because it does not add any useful information, just makes the module name longer. You could use the same name as the extension as module name.
• All the files that you want to be included in the package must be listed in SlicerPKDIA\SlicerPKDIA\CMakeLists.txt. Currently, all the files in the SlicerPKDIALib subfolder are missed, therefore the module would not load into Slicer when installed via the Extensions Manager. It is tempting to add all files in the subfolder using globbing, but it would result in CMake not knowing exactly when a package needs to be rebuilt (e.g., if you add a file to the SlicerPKDIALib subfolder and rebuild the package, CMake would miss the new file). So, I would recommend to list each file.

Not required to fix before merging, but it would make your life easier (more user would be able to successfully use your extension):

• I got the error FileNotFoundError: [Errno 2] No such file or directory: '5: AXIAL T2 SSFSE BH-prod.nii.gz'. This is because node names may be too long and contain invalid characters for filename (in this case :). Images loaded from DICOM usually start with the series number followed by :, so many users would run into this issue. It would be simpler to use a hardcoded filename, but if that is not desirable then you can use qSlicerCoreIOManager.forceFileNameValidCharacters() and qSlicerCoreIOManager.forceFileNameMaxLengthExtension() methods to make the node name suitable as a filename.
• Add link to at least one data set that this module is known to work well on. I've tried it on a random T2 kidney MRI from TCIA (series instance uid: 1.3.6.1.4.1.14519.5.2.1.867044007602064428393129841040266430) and it did not work well. Ideally, register in the SampleData module, as shown in the module template. You can upload a file to your github repository as a release asset if you don't want to rely on an additional site for hosting your sample/test data sets. I've tried the CT segmentation on the Panoramix-cropped data set and the result was not as good as with TotalSegmentator and other models. It is important to provide examples that highlight cases where well-established models like TotalSegmentator don't work that well (I guess TotalSegmentator would struggle segmenting a kidney with severe PKD, while PKDIA may be able to deal with it).
• If dependencies are not installed then this is all the output the user sees: Start ***... Loading inference results.... After this, the Install dependencies button is disabled, so the user cannot install the dependencies (need to restart Slicer). It would be better to at least catch the exception and show a more informative error message. It would be even better if added a little code snippet that detects that not all requirements are installed and ask permission from the user to install them now. After clicking on installing dependencies, pytorch was not found. It asked me to restart Slicer, I restarted, but maybe then I did not click "install dependencies" button again. The procedure is a bit fragile. It is unfortunately a complex topic, maybe just adding a note to the documentation on how to install pytorch if all else fails could be a workaround.

[Jo-Byr]

Hello @lassoan, all points should be fixed. The different bugs were fixed and we added a release with 2 test files.

[lassoan]

Great, thanks for the updates! It simplifies things if the extension name = Slicer+ExtensionName. Would it be possible to rename the repository from https://github.com/conze/SlicerPKDIA to https://github.com/conze/SlicerPolycysticKidneySeg? GitHub makes this really easy (and it automatically adds a redirect from the old name).

The file in the pull request needs to be updated. Its name must match the extension name (PolycysticKidneySeg.json) and if you update the repository name then the scm_url in the file has to be updated accordingly.

It is really hard to find the link to the sample data set. Please add a link to the tutorial section - https://github.com/conze/SlicerPKDIA?tab=readme-ov-file#tutorial It makes getting sample data significantly easier for the user if you add it to the Sample Data module (as shown here). It takes 15 minutes for you, but it saves several minutes for hundreds of interested users.

[Jo-Byr]

Hello @lassoan,

The repository has been renamed and I have modified the pull request file as you wanted. We also added the test files to Sample Data.

[lassoan]

This all looks good now! Let's merge.