1. Information Needed for Segmenting Patient-Specific Abdominal Aortic Aneurysms Using Serial CT Scan Images with Contrast By: Jaime E. Zelaya, Jr. MD/PhD Student, PhD Year I OHSU School of Medicine & Department of Biomedical Engineering Dr. Sandra Rugonyi’s Lab zelaya@ohsu.edu

2. Image Parameters To protect patient privacy, I excluded the patient demographic information from the abdominal CT scan images. Unfortunately, in doing so, other important image information, i.e. image length, is excluded. Thus, I will provide the image parameters specific to the patient of interest on this slide. Should you need more information about the images, please feel free to e-mail me. You may start segmenting at image 41 or a few images before and stop segmentation at the iliac bifurcation which starts at about image 201. Spacing between slices: 1mm DFOV (Dual Field of View): 376mm x 376mm Tilt: 0 Magnification: 1.0x Image matrix: 512 pixels x 512 pixels A few parameter derivations I made include: Pixel size is determined by dividing the DFOV length by the number of pixels. In this case, the pixel size is: 376mm/512pixels = 0.734375mm/pixel The number of pixels in the z-direction can be found by using the slice spacing length and dividing it by the pixel size: 1mm/(0.734375mm/pixel) = about 1.36 pixels. Voxel size ratios in the x, y, and z-direction: 1:1:1.36 (obtained from relationship of the distances of each pixel in the respective directions, 0.73mm:0.73mm:1mm).

3. CT Scan Images Showing Contours used to Obtain Patient-Specific Surface and Fluid Geometrical Models This is a transverse CT scan of a patient’s abdomen. The aortic aneurysm is the ellipsoid structure located at the center of the image. Other nearby structures are identified. Anterior Right Kidney Right Left Kidney Left Posterior Abdominal Aortic Aneurysm (AAA) AAA Lumen Calcifications in AAA wall Vertebral Body & Spine AAA Thrombus The surface contour of the abdominal aortic aneurysm is traced in yellow. To construct surface geometry, I traced the surface contours on every CT scan cross-sectional image and used the coordinates defined in the contour. The lumen contour of the abdominal aortic aneurysm is traced in red. To construct the lumen geometry, I traced the lumen contours on every CT scan cross-sectional image and used the coordinates defined in the contour.

4. Abdominal Aortic Aneurismal Surface Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Top Anterior ViewRight View

5. Abdominal Aortic Aneurismal Surface Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Continued…... Posterior ViewLeft View

6. Abdominal Aortic Aneurismal Surface Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Continued…... Bottom Posterior Right View Note that the structure has open ends.

7. Abdominal Aortic Aneurismal Lumen Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives For this patient, the lumen geometry obtained does not look significantly different in shape when compared to the AAA surface geometry. Top Anterior ViewRight View

8. Abdominal Aortic Aneurismal Lumen Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Continued... Posterior View Left View

9. Abdominal Aortic Aneurismal Lumen Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Continued... Bottom Posterior Right View Note that the lumen geometry also has open ends.

10. Some Difficulties Encountered during the Contour Trace Procedure Sometimes the outer wall is difficult to distinguish from the CT scan because of limited resolution. In such a case, one can draw a contour with a slight distance away from the lumen boundary defined by the contrast. Difficult to Discern AAA Outer Wall Boundary

11. Some Difficulties Encountered during the Contour Trace Procedure for Surface and Lumen Geometries This is the 49 th image in the patient CT scan data that is provided. Notice that part of the bulge of the aneurysm is quite large that it appears next to the celiac trunk/common hepatic artery in addition to its usual location. As one progresses caudally, the cross-section images show how the “divided” aneurysm begins to “merge”. The images shown from left to right are the 52 nd, 55 th, and 61 st images in the provided data series, respectively. Image: 49Image: 55Image: 52Image: 61 Aneurysm Appears Divided in Cross-Section Part of AAA Bulging AAA

12. Some Difficulties Encountered during the Contour Trace Procedure for Surface and Lumen Geometries Continued... Image: 49Image: 52Image: 55Image: 61 In a situation like this, one can either trace surface and lumen contours that gradually grow from image to image until ultimately reaching the desired boundary. If this approach is used, there will be an error in the geometrical representations since important parts of the aneurysm are not considered in some images. I used this approach to generate the aneurismal surface and lumen geometries shown in the previous slides since the program I used for segmentation did not allow me to trace contours in two separate areas. If possible, a more preferable option is to trace the surface and lumen contours for each of the apparently divided parts of the aneurysm to obtain a more accurate representation of the geometry. These serial images show how to trace contours for the generation of a surface geometry in the situation where a cross-section image displays parts of the same large aneurysm separately. The lumen contours can be traced in a similar fashion.

13. After completing the contour tracing process in a program written by one of the post-docs in my laboratory, the output consisted of.obj and.mtl files that included the x, y, and z coordinates for specific points defined within the contours. Then, I opened the.obj file using Mesh Lab, a free downloadable software, to display the geometries shown in this power point presentation. Please feel free to contact me if you need further information or assistance. I look forward to working with you. Thanks for your collaboration.