This document details how to use the best tools and workflows for segmenting the aorta in abdominal Computed Tomography Angiography scans on RedBrick AI.
Project and data setup
Creating a project and importing data
Create the Aorta CTA taxonomy
Let’s start by creating a taxonomy to define what we will annotate. In this project, we’re going to segment the Aorta and Iliac arteries:
- Aortic Tree: Branching system of arteries originating from the aorta, distributing blood throughout the body.
- Common Iliac Artery: Artery bifurcating from the abdominal aorta, dividing into external and internal iliac arteries for the pelvic region and lower limbs.
- External Iliac Artery: Branch of the common iliac artery, continuing as the femoral artery, supplying blood to the lower limbs.
- Internal Iliac Artery: Branch of the common iliac artery, supplying blood to the pelvic organs, gluteal region, and parts of the thigh.
Create an Aorta CTA project using taxonomy
Now, lets create a project with a label and review workflow using the taxonomy we just created.
Upload CTA NRRD data within your project
Now, let’s import a few CTA studies into our project. For this use case, we will use data from the study “AVT: Multicenter aortic vessel tree CTA dataset collection with ground truth segmentation masks”.
Setting up the viewer for CTA
Set up windowing using hanging protocols
When you first open up a case, you’ll notice the windowing settings may not be optimal for viewing and annotating the aorta. Use the windowing shortcut `ctrl` + `left mouse` drag to adjust the windowing settings.
After you find your optimal window width & level, you can set it as the default for your project using RedBrick AI’s hanging protocols. Hanging protocols allows you to pre-configure your viewer with custom scripts; to set windowing, we will use the `setWindowing` function.
Segmenting the aortic tree and arteries
Region growing for aortic tree base segmentation
The aorta is a well-contrasted 3D structure. Therefore, the 3D region growing tool will perform well in segmenting the entire aorta. We’ll first segment the entire aorta as a base segmentation and then use boolean operations to further classify parts of the aorta as iliac arteries.
Cleaning up using 3D scissors, hole-fill, and more
Now that the base segmentation is done, we can perform basic cleanup by using:
- 3D hole filling to fill all small holes in the segmentation.
- 3D scissors on the 3D view to remove large chunks of overflowing segmentations.
- Island removal to only keep the main segmentation structure.
- Dilation (left-click to dilate, right-click to erode) increases our segmentation by 1 pixel in all directions.
Overwrite aorta using boolean operations & masking
Next, we’ll modify the Masking Panel to overwrite only a portion of the aorta segmentation as common, internal, and external iliac arteries.
- Unlock the base aorta segmentation to allow it to be overwritten.
- Create a new common iliac segmentation entity.
- Adjust the masking panel to make Editable area: Inside all segments, and Modify other segments: Overwrite unlocked segments.
- Use the pen tool in the 3D view to overwrite the aorta segmentation with common iliac.