Information Needed for Segmenting PatientSpecific Abdominal Aortic Aneurysms
Information Needed for Segmenting Patient-Specific Abdominal Aortic Aneurysms Using Serial CT Scan Images with Contrast By: Jaime E. Zelaya, Jr. MD/Ph. D Student, Ph. D Year I OHSU School of Medicine & Department of Biomedical Engineering Dr. Sandra Rugonyi’s Lab zelaya@ohsu. edu
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: 1 mm DFOV (Dual Field of View): 376 mm x 376 mm Tilt: 0 Magnification: 1. 0 x 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: 376 mm/512 pixels = 0. 734375 mm/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: 1 mm/(0. 734375 mm/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. 73 mm: 1 mm). • • •
CT Scan Images Showing Contours used to Obtain Patient-Specific Surface and Fluid Geometrical Models Anterior Abdominal Aortic Aneurysm (AAA) Right Kidney Anterior AAA Thrombus AAA Lumen Left Kidney Right Left Calcifications in AAA wall Posterior Vertebral Body & Spine 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. Posterior 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. Posterior 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.
Abdominal Aortic Aneurismal Surface Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Top Anterior View Right View
Abdominal Aortic Aneurismal Surface Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Continued…. . . Posterior View Left View
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.
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 View Right View
Abdominal Aortic Aneurismal Lumen Shell Geometry Obtained for the Given Patient’s Data in Different Perspectives Continued. . . Posterior View Left View
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.
Some Difficulties Encountered during the Contour Trace Procedure Difficult to Discern AAA Outer Wall Boundary 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.
Some Difficulties Encountered during the Contour Trace Procedure for Surface and Lumen Geometries Aneurysm Appears Divided in Cross-Section Image: 49 Image: 52 Image: 55 Image: 61 Part of AAA Bulging AAA 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 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.
Some Difficulties Encountered during the Contour Trace Procedure for Surface and Lumen Geometries Continued. . . These serial images show 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. Image: 49 Image: 52 Image: 55 Image: 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.
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.
- Slides: 13