README.md

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's Keep largest island method to remove noise speckles
• Use Wrap solidify effect (provided by SurfaceWrapSolidify 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: choose Keep largest island option and click Apply

• Select Wrap solidify effect, leave region at default value (Outer surface)

• Reduce Oversampling value to 0.8x in Advancedsection for faster computation and smoother surface (optional)

• Click Apply

Final result: