- Task: Extract skin surface without holes inside the segment. Important for 3D printing or surface-based registration.
- Imaging modality: CT, MRI
Usually there is strong contrast between tissue and air, therefore segmenting the skin surface should be easy, except there may be air inside body part or some tissues or fluids may have image intensity similar to air. Therefore, simple global thresholding may not always work.
This recipe replaces an earlier recipe that used
Flood filling effect. This new recipe is much simpler and provides comparable or better results.
Thresholdand effect to create a segment that contains the head (skin and internal structures)
Keep largest islandmethod to remove noise speckles
Wrap solidifyeffect (provided by
SurfaceWrapSolidifyextension) to fill holes inside the segment.
MRBrainTumor1sample data set
Segment editormodule, create a new segment
Threshold effecteffect, set range from about 110 to maximum (this selects skin surface and structures inside the head), then click Apply
Remove small speckles of noise using
Keep largest islandoption and click
Wrap solidify effect, leave region at default value (
Oversamplingvalue to 0.8x in
Advancedsection for faster computation and smoother surface (optional)