README.md

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 by SurfaceWrapSolidify extension) to extract the brain cavity.
• Use Mask volume effect (provided by SegmentEditorExtraEffects extension) to blank out all non-brain regions in the image.

Example

• Go to Sample Data module and download CT-MR Brain sample data set. 2 MRI and 1 CT volumes are downloaded
• Go to Data module, click on eye icon of CTBrain item in Subject hierarchy tree to see the CT volume.

• Go to Segment editor module, click Add button to create a new segment
• Select Threshold effect and set intensity range of bone (from approximately 300 to maximum value), click Apply

• Remove small speckles of noise using Islands effect: choose Keep largest island option and click Apply

• Select Wrap solidify effect, set region to Largest 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, set Fill value to -1000 (corresponding to air on CT), and click Apply to create a new volume where non-brain region is blanked out. To see the resulting masked volume, click the eye icon next to Output 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 of Segmentation node to hide it, click on eye icon of CTBrain 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: