How to export centerline generated by the VMTK?

Operating system: Linux
Slicer version:4.11.20210226 r29738 / 7a593c8
Expected behavior:
Actual behavior:

Following a recent online tutorial, I was able to generate a centerline of a segemented aorta. I would like to export this centerline to file. Any format is ok, but I basically expect a list of (x,y,z)'s representing the points on the line.

It seems from some older (ie >10 years old) that this was possible as some point, but I don’t know if that’s the case with the latest version of the vmtk toolkit module.

Thanks in advance.

The centerline can be stored either as a markup curve node or as a model node, just save the scene or (in recent Slicer versions) right-click on the centerline in Data module and click “Export to file…”.

Markup curve is saved in json file format, which is simple and self-describing. However, each branch is a separate curve, so if you want to save a complex tree then it is probably better to us a model node. The model node can be saved in many formats, but if you want to preserve the tree structure and all metadata then you need to use .vtk or .vtp format.

Iassoan, thanks for your quick response!

I believe that my version of 3DSlicer, 4.11.20210226, is fairly recent, but when I right-click on the centerline curve or the centerline model in the data module, the only export options listed are to DICOM.

Do I need to install a more recent version of 3D slicer or am I doing something else wrong?


I’m a Slicer developer, so for me 2021-02-26 is very old - a “recent” Slicer version is a Slicer Preview Release that is not older than a few weeks.

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I installed the latest version and then your solution worked like a charm!

Thank you very much for your help (and for the quick responses!)


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