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 bySegmentEditorExtraEffects
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 increaseIntensity tolerance
parameter. If segment leaks inside the tissue then clickUndo
and increaseNeighborhood size
. - Use
Logical operators
effect /Invert
operation to make the segment contain tissue instead of air - Use
Scissors
effect andSmoothing
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 to20
. 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
to3.0
to prevent leaking inside tissue. Click in air region in a slice view.
- Select
Logical operators
effect, operationInvert
, and clickApply
. ClickShow 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, clickApply
to small speckles.
- Select
Smoothing
effect,Median
smoothing method, clickApply
to reduce small random noise on the surface boundary.
Final result: