Add updated skin surface extraction recipe

README.md

@@ -1,8 +1,7 @@
 # Segmentation recipes for 3D Slicer
 
 Recipes for solving common image segmentation tasks using [3D Slicer](https://www.slicer.org).
-
-- [Skin surface extraction](SkinSurface/README.md)
+- [Skin surface extraction](SkinSurface2/README.md)
 - [Craniotomy (splitting segments)](Craniotomy/README.md)
 - [Aorta segmentation (fast, using Fast marching)](AortaFastMarching/README.md)
 - [Aorta segmentation (high-accuracy, using Grow from seeds)](AortaMaskedGrowFromSeeds/README.md)
@@ -19,3 +18,6 @@ External links:
 - Femur and pelvis segmentation from CT:
   - [Video tutorial](https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Image_Segmentation)
 - [Kitware's 3D Slicer segmentation tutorial slides](https://data.kitware.com/#item/5b0f9a308d777f15ebe1fc26)
+
+Obsolete recipes (we have better tools now)
+- [Skin surface extraction using region growing](SkinSurface/README.md)

SkinSurface/README.md

@@ -4,6 +4,8 @@ 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](../SkinSurface2/README.md). 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

SkinSurface2/README.md

@@ -0,0 +1,43 @@
+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](../SkinSurface/README.md). This new recipe is much simpler and provides comparable or better results.
+
+Recommended workflow
+--------------------
+
+- Use `Wrap solidify` effect (provided by `SegmentEditorExtraEffects` extension) with 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
+
+![MRBrainTumor1](image-001.png)
+
+- 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
+
+![Thresholding result.](image-002.png)
+
+- 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 `Advanced`section for faster computation and smoother surface (optional)
+
+- Click `Apply`
+
+![Smoothed result.](image-003.png)
+
+Final result:
+
+![Smoothed result.](image-004.gif)