Hi all, Is-it possible since a “head_T1.nii” to mesh only the scalp by “Segment editor tool” from Python scripts? Thanks in advance, Frederic

There were a couple of small issues. Here is a working version: import SampleData sampleDataLogic = SampleData.SampleDataLogic() masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1() # Create segmentation segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") segment…

If you use Segmentations, “model making” (and real-time updates to the generated 3D mesh) are done automatically. I’ve updated the code sample above to smooth with the correct parameter names and added STL export at the end.

Thanks Andras, I owe you so much.

Hi, Sorry for these 2 new questions: How to save fiducial (F.fcsv) in python? With the wonderful script of @lassoan , I obtain great segmentation of my data (cf. my picture, left part), but I don’t know why there is some mistake during the saving of the stl (cf. my picture, rigth part). This mista…

You can use this function from slicer.util https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/util.py#L423-L439 There are holes in your segmentation. You’ll need to adjust the threshold parameters (likely reducing MinimumThreshold would help)

[image] Frederic: why there is some mistake What mistake you are referring to?

Thanks @cpinter . My data.stl was not like the segmentation mesh, they are all deformated (On my figure, the mesh and the data.stl are in the same point of view). [image]

@lassoan I think he’s referring to the artifacts in the grey model that are caused by the holes. @Frederic In your screenshot it can be seen that the segmentation is not solid (see the holes I was talking about), and those show up inside the head, looking quite strange. Once you fill the holes by a…

@cpinter I dont think that the cause is the holes, the segmentation of Andras script’s have holes too and the data.stl was fine. My script is the same that Andras, I have just change: effect.setParameter(“MinimumThreshold”,“100”) effect.setParameter(“MaximumThreshold”,“2000”) And one of my fil…

The difference between the green and gray is that the green has full opacity, and the gray is semi-transparent, and full opacity hides the holes, semi-transparency lets them show. If you change the segmentation’s opacity to 50% or so, or change the model’s opacity to 100%, then they will look the sa…

Thanks @cpinter , but It’s not that. Below, on the left my data (opacity: 100%, the holes are always here), on the right, the data of the script of Andras (opacity: 70%, with holes too). [Sans titre]

Create a mesh in python script

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Create a mesh in python script

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