- 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.
- SegmentEditorExtraEffects and SurfaceWrapSolidify extensions are installed.
- Head CT image is loaded.
- Create a new segment that will contain the brain region
Thresholdeffect to create a segment that contains the skull bone
Wrap solidifyeffect (provided by
SurfaceWrapSolidifyextension) to extract the brain cavity.
Mask volumeeffect (provided by
SegmentEditorExtraEffectsextension) to blank out all non-brain regions in the image.
- Go to
Sample Datamodule and download
CT-MR Brainsample data set. 2 MRI and 1 CT volumes are downloaded
- Go to
Datamodule, click on eye icon of
CTBrainitem in Subject hierarchy tree to see the CT volume.
- Go to
Segment editormodule, click
Addbutton to create a new segment
Thresholdeffect and set intensity range of bone (from approximately 300 to maximum value), click
Remove small speckles of noise using
Keep largest islandoption and click
Wrap solidify effect, set region to
Split cavitiesand set cavity size slider to approximately 30mm to prevent the segmentation from “leaking” into other soft-tissue regions through small discontinuities in the bone
Mask volumeeffect, set
Fill valueto -1000 (corresponding to air on CT), and click
Applyto create a new volume where non-brain region is blanked out. To see the resulting masked volume, click the eye icon next to
Brain image intensity range is very narrow range compared to whole intensity range of the volume. To see brain contrast better, go to
Datamodule, click eye icon of
Segmentationnode to hide it, click on eye icon of
CTBrain maskednode to show it in slice viewers.
Click “adjust window/level…” toolbar and then hold down
Ctrlkey while click-and-drag in the brain region to set optimal window/level.