Magnetic Resonance Imaging

Our work in Bioimaging develops signal and image processing methods for post-processing of magnetic resonance imaging (MRI) sequences of transplanted organs in humans and small animal models (rats). We work in close collaboration with the NMR Center for Biological Sciences, a NIH supported Center. We process kidney and heart perfusion MRI data, and tagged and untagged cardiac data.

Our work has addressed the following problems: (1) registration and segmentation algorithms for native and transplanted organs (kidney and heart) and their structures; (2) 3D dense displacement and strain maps for the heart with tagged MRI data; and (3) algorithms to monitor the function of transplanted kidneys and hearts.

Our registration and segmentation work is based on energy minimization approaches. For example, in our segmentation work, the energy functional combines several terms that account for smoothness of the contour, local and region based information, and priors on the shape of the organ. We apply level sets to evolve the contours and minimize the energy functional. We relax the relative weights affecting each term of the energy functional.

Segmentation of the heart and its structures in small animals is particularly challenging because of: (1) low contrast; (2) lack of edge information; and (3) the texture of the papillary muscles, which contract during systole to prevent regurgitation of blood into the atria, looks very much like the texture of the myocardium, but clinicians want it segmented out. Our experimental results quite encouraging and of very good quality.

In our 3D work, we derive 3D displacement and strain maps for the heart using MRI tagged data. We describe the heart by a fiber based architecture and model the fiber deformations using continuum mechanics. Details of the approach are in the ISBI 2004 (Chang et al) paper and presentation.

Selected Journal Papers (additional papers in Journal Publications)

  • Ying Sun, Dewen Yang, Qing Ye, Mangay Williams, José M. F. Moura, Fernando Boada, Zhi-Pei Liang, and Chien Ho, “Improving Spatiotemporal Resolution of USPI-Enhanced Dynamic Imaging of Rat Kidneys.” Magnetic Resonance Imaging , 21:6, pp. 593-598, July 2003.
  • Qing Ye, Dewen Yang, Mangay Williams, Donald S. Williams, Charnchai Pluempitiwiriyawej, José M. F. Moura, and Chien Ho, “In-vivo Detection of Acute Rat Renal Allograft Rejection by MRI with USPIO Particles,” Kidney International, 61:3, pp. 1124-1135, March 2002.
  • Dewen Yang, Qing Ye, Mangay Williams, Ying Sun, Tom C.-C. Hu, Donald S. Williams, José M. F. Moura, and Chien Ho, “USPIO-Enhanced Dynamic MRI: Evaluation of Normal and Transplanted Rat Kidneys,” Journal on Magnetic Resonance in Medicine, 46:1152-1163, November 2001.

Selected Conference Papers (additional papers in Conference Publications)

  • Ying Sun, Marie-Pierre Jolly, and José M. F. Moura, “ Contrast-Invariant Registration of Cardiac and Renal MR Perfusion Images,” MICCAI 2004, 7th International Conference on Medical Imaging Computing and Computer Assisted Intervention, Rennes, Saint-Malo, France, September 26-30, 2004.
  • Ying Sun, Marie-Pierre Jolly, and José M. F. Moura, “Integrated Registration of Dynamic Renal Perfusion MR Images,” ICIP’04, IEEE International Symposium on Image Processing, Singapore, October 24-27, 2004.
  • Victor Ha and José M. F. Moura, “Three-dimensional Intrinsic Shapes,” ICIP’04, IEEE International Symposium on Image Processing, Singapore, October 24-27, 2004.
  • Charnchai Pluempitiwiriyawej, José M. F. Moura, Yi-Jen L. Wu, and Chien Ho, “Cardiac MR Image Segmentation: Quality Assessment of STACS,” ISBI’04 IEEE International Symposium on Bioimaging, Arlington, VA, 15-18 April 2004.
  • Hsun-Hsien Chang, José M. F. Moura, Yijen L. Wu, Kazuya Sato, and Chien Ho, “Reconstruction of 3D Dense Cardiac Motion from Tagged MR Sequences,” ISBI’04 IEEE International Symposium on Bioimaging, Arlington, VA, 15-18 April 2004.
  • Ying Sun, José M. F. Moura, and Chien Ho, “Subpixel Registration in Renal Perfusion MR Image Sequence,” ISBI’04 IEEE International Symposium on Bioimaging, Arlington, VA, 15-18 April 2004.
  • Ying Sun, Marie-Pierre Jolly, and José M. F. Moura, “Integrated Registration of Dynamic Renal Perfusion MR Images,” submitted for publication, February 2004.
  • Yijen L. Wu, Kazuya Sato, Ying Sun, Hsun-Hsien Chang, Kevin Hitchens, José M. F. Moura, and Chien Ho, “Non-Invasive Early Detection of Acute Cardiac Allograft Rejection by MRI in Rodent Model,” 12th ISMRM, Twelfth Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, Kyoto, Japan, May 15-21, 2004.
  • Yijen L. Wu, Kazuya Sato, Ying Sun, Hsun-Hsien Chang, J. Williams, Kevin Hitchens, José M. F. Moura, and Chien Ho, “The Two Pronged Approach for Non-Invasive Early Detection of Acute Cardiac Allograft Rejection by MRI in a Rodent Transplantation Model,” 12th ISMRM, Twelfth Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, Kyoto, Japan, May 15-21, 2004.
  • Charnchai Pluempitiwiriyawej, José M. F. Moura, Yi-Jen L. Wu, Shinichi Kanno, and Chien Ho, “Automatic Segmentation for Cardiac MR Image Sequence,” SCMR’04 The Seventh Annual Society for Cardiovascular Magnetic Resonance Scientific Sessions, Barcelona, Spain, February 13-15, 2004.
  • Yijen L. Wu, Kazuva Sato, Ying Sun, José M. F. Moura, and Chien Ho, “Noninvasive Early Detection of Acute Cardiac Allograft Rejection by MRI,” SCMR’04 The Seventh Annual Society for Cardiovascular Magnetic Resonance Scientific Sessions, Barcelona, Spain, February 13-15, 2004.
  • Charnchai Pluempitiwiriyawej and José M. F. Moura, “Stochastic Active Contour for Cardiac MR Image Segmentation,” ICIP’03, IEEE International Conference on Image Processing, Barcelona, Spain, September 2003.
  • Ying Sun, Dewen Yang, Qing Ye, Chien Ho, and José M. F. Moura, “Dense Motion Estimation in Tagged MRI Sequence,” Eleventh Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, ISMRM, Toronto, ON, Canada, July 10-17, 2003.
  • Ying Sun, José M. F. Moura, Dewen Yang, and Chien Ho, “Kidney segmentation in MRI Sequences Using Temporal Dynamics,” IEEE International Symposium on Bioimaging, pp. 98-101, Washington DC, July, 2002.
  • Ying Sun, Dewen Yang, Qing Ye, Chien Ho, and José M. F. Moura, “Pseudo-Color Visualization of Dynamic Renal Perfusion in MRI,” Tenth Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, ISMRM, Honolulu, Hawaii, May 19-24, 2002.
  • Qing Ye, Dewen Yang, Ying Sun, Mangay Williams, Ben Y. Tseng, José M. F. Moura, and Chien Ho, “Reduction of Renal Ischemia/ Reperfusion Injury Using Anti-Apoptosis Treatment with Pan-Caspase Inhibitor, MX1122,” American Transplant Congress, 2002.
  • Q. Ye, D. Yang, M. Williams, D. S. Williams, C. Pluempitiwiriyawej, J. M. F. Moura, and C. Ho, “In-Vivo Detection of Acute Rejection of Rat Renal Allograft by MRI with Ultrasmall Superparamagnetic Iron Oxide Particles,” Ninth Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, ISMRM/ESMRMB Joint Annual Meeting, Glasgow, Scotland, April 21 –27, 2001.
  • Y. Sun, D. Yang, Q. Ye, C. Ho, and José M. F. Moura, “A Novel Approach in Analyzing Dynamic Intrarenal Signals Using USPIO and MRI,” Ninth Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine, ISMRM/ESMRMB Joint Annual Meeting, Glasgow, Scotland, April 21 –27, 2001.

Selected Seminars and Talks

  • Hsun-Hsien Chang, José M. F. Moura, Yijen L. Wu, Kazuya Sato, and Chien Ho, “Reconstruction of 3D Dense Cardiac Motion from Tagged MR Sequences,” ISBI’04 IEEE International Symposium on Bioimaging, Arlington, VA, 15-18 April 2004. [PDF]
  • José M. F. Moura, “MRI Techniques for Noninvasive Monitoring of Transplanted Organs,” Siemens Corporate Research, July 31, 2003. [PDF]

Lab Members

  1. Charnchai Pluempitiwiriyawej
  2. Ying Sun
  3. Hsun-Hsien Chang
  4. Roger Kumar