README.md

Overview

• Task: Segment aorta on CT. This method produces results quickly, without requiring too much user input. The same method can be used for segmenting other structures that have a good contrast compared to the background but there are other structures with similar intensity nearby.
• Imaging modality: any

Prerequisites

• SegmentEditorExtraEffects extension is installed.
• Contrast-enhanced CT volume is loaded.

Recommended workflow

• Click Paint effect and paint a few strokes inside the aorta.
• Click Fast Marching effect.
• Set Maximum volume to 1% (since volume of the aorta is very small compared to the total volume of the CT image).
• Click Initialize to compute segmentation preview.
• Adjust segment volume slider to achieve complete segmentation, but not too high value (to prevent leaking out of the aorta).
• Click Apply when segmentation preview is satisfactory to finalize the segmentation.
• Apply Smoothing effect, Median method to fill in missed voxels and smooth outer surface of the vessel.

Tips:

• If Fast Marching not visible then install SegmentEditorExtraEffects extension and restart the application
• To make paint strokes more visible, you can deactivate Paint effect and left-click-and-drag in the slice view to change background volume window/level.
• To see preview in 3D view: Click the down-arrow button on the right side of Show 3D button and disable Surface smoothing (this will make updates of 3D visualization very fast). Click Show 3D button.
• If a large piece of the aorta is missed then click Cancel, use Paint effect to paint inside the area that is missing, then re-initialize Fast Marching effect as described above.

Example

• Download CTACardio sample data set
• Go to Segment editor module, click Add button to create a new segment
• Select Paint effect and paint a few strokes inside the aorta.

• Click Fast Marching effect
• Set Maximum volume to 1% (since volume of the aorta is very small compared to the total volume of the CT image)
• Click Initialize to compute segmentation preview.
• Adjust segment volume slider to achieve complete segmentation, but not too high value, to prevent leaking out of the aorta.

• To see preview in 3D view: Click the down-arrow button on the right side of Show 3D button and disable Surface smoothing, then click Show 3D button.

• Click Apply when segmentation preview is satisfactory.
• Apply Smoothing effect, Median method to fill in missed voxels and smooth outer surface of the vessel.

Final result: