- 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.
Flood fillingeffect (provided by
SegmentEditorExtraEffectsextension) 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 toleranceparameter. If segment leaks inside the tissue then click
Logical operatorseffect /
Invertoperation to make the segment contain tissue instead of air
Smoothingeffect to remove artifacts and noise
MRBrainTumor1sample data set
- Go to
Segment editormodule, create a new segment
- Click anywhere in a slice view in air region (outside tissues) => Not all the air region is included in the segment
Intensity toleranceparameter to
20. Click in air region in a slice view. => Segment leaked inside the tissue.
Undoto undo the last flood filling operation.
3.0to prevent leaking inside tissue. Click in air region in a slice view.
Logical operatorseffect, operation
Invert, and click
Show 3Dto see segmentation result in 3D viewer.
Scissorseffect and outline areas in the 3D view that were incorrectly included in the segment (due to image artifacts)
Keep largest islandmethod, click
Applyto small speckles.
Mediansmoothing method, click
Applyto reduce small random noise on the surface boundary.