Overview
- Task: Skull stripping - remove all skull and all other bone and soft tissues around the brain. Can be used whenever a fairly homogeneous region needs to be extracted from an image volume that is mostly surrounded by different intensity regions.
- Imaging modality: head CT.
Prerequisites
- SegmentEditorExtraEffects and SurfaceWrapSolidify extensions are installed.
- Head CT image is loaded.
Recommended workflow
- Create a new segment that will contain the brain region
- Use
Threshold
effect to create a segment that contains the skull bone - Use
Wrap solidify
effect (provided bySurfaceWrapSolidify
extension) to extract the brain cavity. - Use
Mask volume
effect (provided bySegmentEditorExtraEffects
extension) to blank out all non-brain regions in the image.
Example
- Go to
Sample Data
module and downloadCT-MR Brain
sample data set. 2 MRI and 1 CT volumes are downloaded - Go to
Data
module, click on eye icon ofCTBrain
item in Subject hierarchy tree to see the CT volume.
- Go to
Segment editor
module, clickAdd
button to create a new segment - Select
Threshold
effect and set intensity range of bone (from approximately 300 to maximum value), clickApply
-
Remove small speckles of noise using
Islands
effect: chooseKeep largest island
option and clickApply
- Select
Wrap solidify effect
, set region toLargest cavity
- Enable
Split cavities
and set cavity size slider to approximately 30mm to prevent the segmentation from “leaking” into other soft-tissue regions through small discontinuities in the bone - Click
Apply
- Select
Mask volume
effect, setFill value
to -1000 (corresponding to air on CT), and clickApply
to create a new volume where non-brain region is blanked out. To see the resulting masked volume, click the eye icon next toOutput volume
.
-
Brain image intensity range is very narrow range compared to whole intensity range of the volume. To see brain contrast better, go to
Data
module, click eye icon ofSegmentation
node to hide it, click on eye icon ofCTBrain masked
node to show it in slice viewers. -
Click “adjust window/level…” toolbar and then hold down
Ctrl
key while click-and-drag in the brain region to set optimal window/level.
Final result: