Dear all, I hope you guys can help. I’m relatively new to 3D slicer. I am using the 4.11 version. My goal is to compute skeletal muscle area in a single CT-slice. I have loaded the CT and have created a segment using the segment editor. I manually outlined all the muscles in a single segment. If …

We developed a module for this with @hherhold some time ago, now I’ve touched it up and pushed it into Sandbox extension . You can download it tomorrow in latest Slicer Preview Release. The Sandbox extension is in Examples category, after you install it, the “Segment Cross-Section Area” module should…

Dear Andras, Thanks very much for your quick reply and solution! Once the module is available I’ll try it out. Best, Justin

Nightly build was not successful on Windows last night but tomorrow it should be OK. If you want to try it earlier then you can download the repository from github and add the SegmentCrossSectionArea folder to the additional module paths in Slicer application settings.

Thanks very much Andras, I noticed the windows version wasn’t updated, but I was able to install the module manually with your instruction. I also found out that I could filter out the relevant HU range using the section editor, so I have all I need. Thanks again, Best, Justin

Can the SegmentCrossSectionArea also be reached through script? I’ve looked up the script and tried areaNode = slicer.mrmlScene.AddNewNodeByClass(“SegmentCrossSectionAreaWidget(ScriptedLoadableModuleLogic)”) tableNode = slicer.mrmlScene.AddNewNodeByClass(“vtkMRMLTableNode”, “Segment cross-section…

The module’s automatic test serves as an example of how to use the module from a script: PerkLab/SlicerSandbox/blob/90320348677225ae86bb54d0dea563af55c5bcae/SegmentCrossSectionArea/SegmentCrossSectionArea.py#L494-L496 logic = SegmentCrossSectionAreaLogic() logic.run(segmentationNode, mast…

Thanks, I found the example but I did not know I needed to import As you say, I just followed the rest of the test module to work run the model from script.

Compute surface area in segment based on Hounsfield units (CT-images)

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lassoan (Andras Lasso) Split this topic April 21, 2020, 3:38pm 6

A post was split to a new topic: Automating thresholding of existing segments

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Compute surface area in segment based on Hounsfield units (CT-images)

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