Overview
- 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.
Recommended workflow
- Use
Threshold
and effect to create a segment that contains the head (skin and internal structures) - Use
Islands
effect’sKeep largest island
method to remove noise speckles - Use
Wrap solidify
effect (provided bySurfaceWrapSolidify
extension) to fill holes inside the segment.
Example
- Download
MRBrainTumor1
sample data set
-
Go to
Segment editor
module, create a new segment -
Select
Threshold effect
effect, 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
Islands
effect: chooseKeep largest island
option and clickApply
-
Select
Wrap solidify effect
, leave region at default value (Outer surface
) -
Reduce
Oversampling
value to 0.8x inAdvanced
section for faster computation and smoother surface (optional) -
Click
Apply
Final result: