Segmenting the aorta and iliac arteries in abdominal CTA scans

Shivam Sharma

January 20, 2024

Request Access to F.A.S.T.⚡

Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.

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

Skip to Segmenting the aortic tree and arteries section to directly see the annotation part of this guide.

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:

  1. Aortic Tree: Branching system of arteries originating from the aorta, distributing blood throughout the body.
  2. Common Iliac Artery: Artery bifurcating from the abdominal aorta, dividing into external and internal iliac arteries for the pelvic region and lower limbs.
  3. External Iliac Artery: Branch of the common iliac artery, continuing as the femoral artery, supplying blood to the lower limbs.
  4. Internal Iliac Artery: Branch of the common iliac artery, supplying blood to the pelvic organs, gluteal region, and parts of the thigh.
Aorta anatomy

Please visit our documentation for instructions on creating taxonomies.

Create an Aorta CTA project using taxonomy

Now, lets create a project with a label and review workflow using the taxonomy we just created.

Please visit our documentation for instructions on creating projects.

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

Please visit our documentation to understand the basics of our viewer.

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:

  1. 3D hole filling to fill all small holes in the segmentation.
  2. 3D scissors on the 3D view to remove large chunks of overflowing segmentations.
  3. Island removal to only keep the main segmentation structure.
  4. 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.

  1. Unlock the base aorta segmentation to allow it to be overwritten.
  2. Create a new common iliac segmentation entity.
  3. Adjust the masking panel to make Editable area: Inside all segments, and Modify other segments: Overwrite unlocked segments.
  4. Use the pen tool in the 3D view to overwrite the aorta segmentation with common iliac.