Hello Slicer Community, I have some scripts written for a client about 9 or 10 years ago for automated centerline extraction (and calculating metrics for those centerlines) that I developed with VMTK. The client recently decided they wanted to start using this functionality again (I don’t think th…

From my understanding of the documentation and this comment from the man himself, yes unless you need the slicer modules. SlicerPython is like a prepackaged virtual environment, it includes vmtk and can be run from cmd but you’ll need to have the user interface open for access to slicer.app, slicer…

Thank you Kyle, I missed that page in the documentation though, it’s mostly geared towards using scripts inside of Slicer but between that and Andras’ comment it seems like I figured out how to get my dependencies added but still I get this error: from vmtk import vtkvmtk ModuleNotFoundError: …

Thank you Kyle, Looks like I’m missing the SlicerVMTK extension. Kyle, did you install it via the install.sh script in the docker examples or somehow directly?

I downloaded the compressed files for each extension I needed from the slicer extension catalogue and then ran the following in the slicer console: slicer.app.extensionsManagerModel().installExtension('/path/to/myextension.zip')

It looks like I was able to get the SlicerVTMK extension to install (after adding many apt-get calls to the docker container. So I have something like this in install.h ... echo "Install SlicerVMTK extension" $slicer_executable -c ' em = slicer.app.extensionsManagerModel() extensionName = "SlicerV…

Different approach for centerline extraction

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wesselk (Kyle) February 1, 2024, 5:15pm 4

I ran into that same problem and made another post which got great answers, hopefully it helps.

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Different approach for centerline extraction

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