Hi, I’m using 3D Slicer for tooth segmentation and I’ve created an stl model from ct scan (DICOM). I’ve done that using Segment editor module. Can someone tell me which segmentation algorithm is used in slicer to create an stl model from ct scan?

If you mean which algorithms are used for generating closed surface from binary labelmap representation of the segmentation: see implementation here . In short: vtkDiscreteFlyingEdges3D followed by vtkWindowedSincPolyDataFilter , vtkDecimatePro (optional), and vtkPolyDataNormals .

[image] sara04: I’ve created an stl model from ct scan (DICOM) [image] sara04: which segmentation algorithm is used in slicer to create an stl model from ct scan I don’t understand the question. You said you did all that. Am I misunderstanding something?

I need to write some theory about image segmentation and the things I’ve done in 3D Slicer. Since I used thresholding, I wanted to know the names of algorithms you used in implementation ( eg. k-means clustering). I’m a student and new to this so I don’t understand this very well. It will be very h…

Thank you @lassoan , I think you get my point. So, you used marching cubes algorithm and flying edges? I need to write something about this algorithms and I really want to write about algorithms that are implemented in slicer.

We did not use matching cubes. We used flying edges algorithm instead because it is faster. You can find description of the methods at the associated links.

I see, thanks! Andras gave you the details, but if you’re looking for some text, then I can send you my PhD thesis in which these are described in detail (it will be publicly accessible in a few weeks but I can send you an unofficial copy).

Thank you, that was really helpful!

@lassoan @cpinter Hi, I have another problem. I have done tooth segmentation and I extracted two stl files, tooth crown and root . [image] My question is… Is it possible to do an automatic segmentation of the contact surface between two volumes in contact (crown and root ) that were themselves co…

You can export segments to models and then use “Model to model distance” extensions to compute distance between them. You can visualize the distance using color mapping or set a threshold value to show only parts that are closer to each other than the chosen threshold value (in Models module / Displ…

I got this [image] and then i set a threshold value to get this [image] Is it possible to save this last surface as stl file? I tried to save it but when I load it, i got the whole crown (first picture), not the surface I wanted.

Adjusting display options in Models module does not alter the model’s geometry, just modifies display settings. You can create a new model node from the displayed thresholded model by copy-pasting this line into the Python console: slicer.modules.models.logic().AddModel(getNode('sphere').GetDisplay…

Segmentation algorithm used in 3D Slicer

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Segmentation algorithm used in 3D Slicer

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