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Advanced MR Imaging Techniques for Tumor and Edema Segmentation: Insights from Research

In Week 2 of my research experience, I focused on MR imaging and terminology, analyzing brain tumor and edema segmentation through a foundational paper that discussed an integrated Bayesian model. I collected MR images from multiple patients and noted significant differences between T1 and FLAIR images, primarily in edema detection. The initial algorithm involved subtracting T1 pixels from FLAIR, applying Otsu’s auto-thresholding to refine segmentation. Future steps include using ITK for mutual information-based registration and exploring various segmentation techniques, such as geodesic active contours.

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Advanced MR Imaging Techniques for Tumor and Edema Segmentation: Insights from Research

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  1. Vision REU Week 2 Ben Schoepke

  2. Research • MR physics and terminology • Found paper that attempted both tumor and edema segmentation Corso, JJ, Sharon, E., Yuille, A.: Multilevel segmentation and integrated bayesian model classification with an application to brain tumor segmentation. MICCAI 9 (2) (2006) 790-8 T1 T1E T2 FLAIR Ben Schoepke REU Week 2 6/1/07

  3. Experimentation • Obtained MR images from multiple patients Ben Schoepke REU Week 2 6/1/07

  4. Experimentation • Noticed only major difference between T1 and FLAIR was edema T1 FLAIR Ben Schoepke REU Week 2 6/1/07

  5. Experimentation • Initial algorithm: subtract T1 pixels from FLAIR FLAIR T1 Ben Schoepke REU Week 2 6/1/07

  6. Experimentation • Initial algorithm: subtract T1 pixels from FLAIR • Use Otsu’s auto-thresholding method: Flair – T1 image with Otsu threshold applied Result overlayed on FLAIR image Ben Schoepke REU Week 2 6/1/07

  7. Problems Edema not well defined T1 FLAIR - not edema? Ben Schoepke REU Week 2 6/1/07

  8. Establishing ground truth Ben Schoepke REU Week 2 6/1/07

  9. Next week • Start using ITK • Implement mutual information-based image registration Source: Eric and Pinkung’s paper Ben Schoepke REU Week 2 6/1/07

  10. Next week • Experiment with different segmentation techniques Source: ITK documentation Geodesic active contours segmentation Original image Canny-edge level set segmentation Ben Schoepke REU Week 2 6/1/07

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