I added video tutorials on how to register and fuse and segment cochlea multi-modal images using our VisSim Tools extension that uses elastix toolbox as well. The source code can be found here . Sample cochlea datasets are also shared and can be downloaded using “Data Store” module. This is still …

The SlicerCochlea extension is already merged few days ago but it does not appear in the extension manager. Is there something wrong?

It does appear in the extension manager for me with the current nightly build on Linux (4.11.0-2018-10-23 r27518), but it doesn’t seem to work. I’m getting the following error messsage in the terminal window where I start Slicer: $ slicer Traceback (most recent call last): File "<string>", line 1…

Thanks for interesting in our work. I tested it on Slicer 4.81. I will update it and test it on the recent versions 4.10 and 4.11 next week. Not sure why Tkinter does not work, maybe Slicer 11 uses python 3? I just updated the code, hopefully, this problem is fixed in the next build.

Thanks for the info. I will remove Tkinter and tk from the code.

The extension is updated and it should work with recent slicer version 4.10 and 4.11 when it builds next time. I don’t know why the extension icon and screenshots do not appear, is there something I should do to fix it?

Icon URLs in s4ext file are not used, they are for information purposes only. What matters is the URLs in the CMakeLists.txt file ( https://github.com/MedicalImageAnalysisTutorials/SlicerCochlea/blob/master/CMakeLists.txt ). Also, URL seems incorrect. URL to raw data on github usually looks like this…

Thanks, Andras, now it is clear. I updated the links with raw links in both s4ext and CMakeLists.txt.

Ok, I installed the latest Slicer 3D nightly for Linux, and now I’m getting this error on the terminal after picking a point in the middle of the cochlea in a CT image, and then clicking on “Run”: Switch to module: "CochleaSeg" ======================================================= Automatic…

Thanks for testing. I could not reproduce the problem. Does the cochlea registration module work? Please try these steps: save your cochlea image in your home folder as nrrd format. Sometimes elastix does not recognize filenames with special characters or spaces, e.g. use this filename. /home…

VisSim Cochlea Tools extension is now public

Support

jamesobutler (James Butler) October 24, 2018, 3:15pm 5

@brhoom Slicer is not using python 3 yet, but you might want to review the comment in this thread Should we do something about EM segmenter?. TCL support was recently disabled in Slicer.

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VisSim Cochlea Tools extension is now public

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