README.md

Overview

• Task: Extract skin surface without holes inside the segment. Important for 3D printing or surface-based registration.
• Imaging modality: CT, MRI

Important: This recipe is now obsolete. It is replaced by a new recipe that uses Wrap solifidy effect. The new recipe is much simpler and provides comparable or better results as this one.

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.

Recommended workflow

• Use Flood filling effect (provided by SegmentEditorExtraEffects extension) to segment outside air. Click anywhere in the outside air in slice views to segment the air. If not all areas are hightlighted then click in air regions that are not included and/or increase Intensity tolerance parameter. If segment leaks inside the tissue then click Undo and increase Neighborhood size.
• Use Logical operators effect / Invert operation to make the segment contain tissue instead of air
• Use Scissors effect and Smoothing effect to remove artifacts and noise

Example

• Download MRBrainTumor1 sample data set

• Go to Segment editor module, create a new segment
• Select Flood filling effect
• Click anywhere in a slice view in air region (outside tissues) => Not all the air region is included in the segment

• Increase Intensity tolerance parameter to 20. Click in air region in a slice view. => Segment leaked inside the tissue.

• Click Undo to undo the last flood filling operation.
• Increase Neighborhood size to 3.0 to prevent leaking inside tissue. Click in air region in a slice view.

• Select Logical operators effect, operation Invert, and click Apply. Click Show 3D to see segmentation result in 3D viewer.

• Select Scissors effect and outline areas in the 3D view that were incorrectly included in the segment (due to image artifacts)

• Select Islands effect, Keep largest island method, click Apply to small speckles.

• Select Smoothing effect, Median smoothing method, click Apply to reduce small random noise on the surface boundary.

Final result: