Master's Thesis

Deformable Registration of Cine-MRI Images for Colonic Motility Analysis
Project by: Raphael Arias and Arianne Tran
Advisor: Prof. Nassir Navab
Supervision by: Mehmet Yigitsoy
Due date:

Abstract

Functional gastrointestinal disorders such as chronic diarrhea are chronic conditions presenting with a significant socioeconomic burden and are usually associated with the colonic motility dysfunction. Therefore, it is necessary to study colonic motility in order to understand its effects on such conditions leading to an improved and more adequate therapy in the end. Existing techniques such as manometry or scintigraphy are either invasive and have long examination times or expose patients to ionizing radiation creating demand for a fast and non-invasive monitoring technique for the quantification of colonic motility. Functional cine magnetic resonance imaging (MRI) allows for noninvasive, fast dynamic imaging with a high tissue contrast. It provides the possibility to observe both anatomical and functional properties of the colon. Current analysis techniques are based on diameter measurements of colonic lumen on cine-MR images for which a segmentation of the colon is necessary. However, in order to do a segmentation, the respiratory motion has to be compensated and segmentation has to be initialized for each frame which is possible by employing a registration algorithm. In this project, affine and deformable registration algorithms for the registration of cine-MR images will be implemented and integrated into an existing analysis framework.

Tasks

The first phase of the thesis involves the development of a registration technique for the affine alignment of frames in a cine-MRI sequence. An existing affine registration method will be integrated into the colon motility analysis framework. After successful completion of the first phase, a deformable registration algorithm will be implemented and integrated into the same framework.

Resources

• Good programming skills in C++, Matlab and other languages
• Working experience with frameworks (ITK, VTK, Qt)
• Interest in deformable image registration

Contact

Mehmet Yigitsoy.

Groupwise Deformable Registration	Diameter Measurements on Cine-MR Images 1	Diameter Measurements on Cine-MR Images 2

Literature

	M. Yigitsoy, C. Wachinger, N. Navab Temporal Groupwise Registration for Motion Modeling Information Processing in Medical Imaging (IPMI), July 3-8 2011. (bib)
	M. Yigitsoy, M. Reiser, S. Kirchhoff, N. Navab Out-of-plane Motion Compensation in Cine-MRI The 4th MICCAI Workshop on Computational and Clinical Applications in Abdominal Imaging (MICCAI-ABD 2012), Nice, France, Oct 1, 2012 (bib)
	M. Yigitsoy, M. Reiser, N. Navab, S. Kirchhoff Dynamic Graph Cuts for Colon Segmentation in Functional Cine-MRI IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2012), Barcelona, Spain, May 2 - 5, 2012 (bib)
	O. Kutter, S. Kirchhoff, M. Berkovic, M. Reiser, N. Navab Spatio-temporal registration in multiplane MRI acquisitions for 3D Colon Motiliy analysis SPIE Medical Imaging, San Diego, California, USA, 16-21 February 2008 (bib)
	C. Harrer, S. Kirchhoff, A. Keil, C. Kirchhoff, T. Mussack, A. Lienemann, M. Reiser, N. Navab Semi-automatic detection of Gd-DTPA-saline filled capsules for colonic transit time assessment in MRI Proc. of SPIE Medical Imaging, San Diego, California, USA, February 2008. (bib)
	B. Glocker, S. Buhmann, C. Kirchhoff, T. Mussack, M. Reiser, N. Navab Towards a Computer Aided Diagnosis System for Colon Motility Dysfunctions SPIE Medical Imaging, San Diego, California, USA, 17-22 February 2007 (bib)