Overview

• Task: Cut a hole on the skull to simulate a craniotomy. The same method can be used anytime a segment has to be partitioned to multiple segments.
• Imaging modality: any

Prerequisites

Have a segment that need to be cut/partitioned into multiple pieces.

Recommended workflow

• Create a new segment that will contain the parts separated from the existing segment
• Click Show 3D button to see the segment in 3D
• Use Scissors effect with Fill inside option to cut a hole
• Rotate view, select original segment, and use Scissors effect again to add back regions to the original segment that should not have been cut out (e.g., other side of the skull)

Example

• Download CT-MR Brain sample data set
• Go to Data module, select MRBrainT1 and MRBrainT2 data sets, right-click and delete them (we will not use the MRI images)

• Go to Segment editor module, click Add button to create a new segment
• Select Threshold effect, set 100.00 as lower threshold, and click Apply

• Click Show 3D button to see the segmented bone in 3D viewer.

• Click Add button to create a new segment, which will store the part that is separated from the skull
• Select Scissors effect
• Set Operation to Fill inside, as we will use scissors to fill new empty segment
• Scroll down to Masking section and change Editable area to Inside all segments so that we do not add any new regions to segments, just allow editing within existing segments and outline areas in the 3D view that were incorrectly included in the segment (due to image artifacts)
• Mark the boundary of the craniotomy in the 3D view by using the left mouse button

• Press space key to deactivate Scissors effect
• Click the eye icon of Segment_1 to hide the skull and rotate the 3D view by about 90 degrees. Scissors effect cut through the entire volume, so it created two holes. We will remove the hole on the other side of the skull by adding it to the first segment.
• Select Segment_1 in the segment list becase we will add back parts from Segment_2
• Press space key to activate Scissors effect
• Draw a curve around the parts of the segment that needs to be added back to the skull.

• Press space key to deactivate Scissors effect
• Click the eye icon of Segment_1 to show the skull, and click the eye icon of Segment_2 to show the cutout bone

Final result: