Thanks Andras. Your suggestion helped a lot and we were able to generate a 3D stl file. However a new issue has arisen.
The stl file so obtained does not have a smooth surface. It is composed of blocks (like a pixelated image) and is therefore unsuitable for printing. Can you tell us how to overcome this problem.
You have three options, you can use all, but the first one is the most important:
- crop your input volume to the region of interest & resample to have sufficiently high resolution using the
Crop volume module: specify your ROI, select
Isotropic spacing, select sufficiently low
spacing scale value (the lower the value, the more details you can preserve during segmentation, but more memory and processing time you will need; typically 0.5 … 0.2 should work), select bspline interpolator
- smooth the labelmap representation using
Smoothing effect in Segment editor module
- smooth the generated surface: in Segment editor module, click on the small arrow on the “Show 3D” button, choose
Set surface smoothing, and increase the smoothing value. (in older Slicer versions, this setting was only available in Segmentations module: click
Update button in the row of
Closed surface representation in
Representations section, click on
Binary labelmap -> Closed surface rule, increase
Smoothing factor value)