Add SlicerRadioembolizationDosimetry Extension

[4burakfe]

New extension

SlicerRadiembolizationDosimetry. A module pack that allows users to perform voxel-based dosimetry with patient-relative and absolute calibration methods for treatments of liver tumors with radioactive microspheres.

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)
• Documentation, tutorial, and test data are provided for most modules. A tutorial provides step-by-step description of at least the most typical use case, include a few screenshots. Any sample data sets that is used in tutorials must be registered with the Sample Data module to provide easy access to the user.
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Tier 5

Critically important extensions, supported by Slicer core developers. New Slicer Stable Release is released only if all Tier 5 extension packages are successfully created on all supported platforms.

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• Automated tests for all critical features.
• Maintainers respond to questions related to the extension on the Slicer Forum.
• All requirements of tiers < 5.

[4burakfe]

Sorry for the missing Cmakelist files and wrong extension architecture. I have updated the repository to fit the requirements.

[4burakfe]

Any updates? I am waiting for this to upload another extension.
Best regards...

[lassoan]

Thank you very much for your contribution. The extension looks very nice!

I wanted to go through your tutorial, but I got stuck at the very first step "Load SPECT or PET volume.". Could you please provide sample data set that are known to work well with your modules and anybody who is interested could use for testing? The best is to register the sample data sets to "Sample Data" module - as it is shown in the module template, but at least provide a direct download link in the tutorial. Often it is quite difficult to download sample data set from TCIA or other public data hosting sites, so I would recommend to upload the sample data set as release asset into your github repository (similarly to this).

[4burakfe]

@lassoan Thank you for your kind reply.
Here I have uploaded some sample images: https://github.com/4burakfe/SlicerRadioembolizationDosimetry_SampleImages/releases/tag/TestImages
I have also changed the readme file and added reference to the sample image repository
Thank you for your time

[4burakfe]

Any updates? It has been four and a half months since I have uploaded the extension. I am waiting for this to upload another extension. Thank you for your understanding :)
Best regards

[lassoan]

Thank you for your patients. It looks great, I just submitted a pull request with some fixes:

4burakfe/SlicerRadioembolizationDosimetry#1

If you merge it then it should be ready to be added to the Extensions Index.

Further recommendations:

Common:

• qMRMLSegmentSelectorWidget already contains a segmentation node selector. You can remove the separate segmentation node selector.

LSF Calculator:

• Neither of the sample data sets contains lung segment. Add sample data that can be used to test this module.

RadioembolizationDosimetry – Patient Relative:

• Provide "Define:" values that can be used for at least one of the sample data sets in documentation

RadioembolizationDosimetry – Absolute:

• Provide "Input:" values that can be used for at least one of the sample data sets in documentation

EasyReg:

• Permanently altering an input image should be generally avoided. I would recommend to just let the user specify the two ROIs and then when the user clicks "Register images" then create temporary cropped volumes, register them, and then delete the cropped volumes. The computed transformation can be applied to the full volume (but it is also OK to create a new resampled output volume).
• Do not automatically delete the ROI that the user created. Permanently deleting something that the user spent his time to create is frustrating. Also, the user cannot make any corrections - slightly change the ROI when he realizes that he cropped more or less than actually needed - and perform the operation again.
• When the user places the ROI he already sets the position and size. It is frustrating that all this work is lost when the user selects that ROI in the node selector. Instead, you can add a button to fit the ROI to the volume (that button could automatically create a new ROI as well, if one is not selected already).

[4burakfe]

Thank you very much for your interest and effort. I have merged the pull request with your changes and I will update the extension as soon as possible with your recommendations.

[lassoan]

Thank you! Your extension should show up in the Extensions Manager in Slicer Preview Release from tomorrow.

[lassoan]

I've also submitted this to the Extensions Manager in the Slicer Stable Release (#2205).