SLIMMER: SLIce MRI motion estimation and reconstruction tool for studies of fetal anatomy

Kio Kim; Piotr A. Habas; Vidya Rajagopalan; Julia Scott; Francois Rousseau; A. James Barkovich; Orit A. Glenn; Colin Studholme

doi:10.1117/12.878489

11 March 2011 SLIMMER: SLIce MRI motion estimation and reconstruction tool for studies of fetal anatomy

Kio Kim, Piotr A. Habas, Vidya Rajagopalan, Julia Scott, Francois Rousseau, A. James Barkovich, Orit A. Glenn, Colin Studholme

Author Affiliations +

Proceedings Volume 7962, Medical Imaging 2011: Image Processing; 79624D (2011) https://doi.org/10.1117/12.878489
Event: SPIE Medical Imaging, 2011, Lake Buena Vista (Orlando), Florida, United States

Abstract

We describe a free software tool which combines a set of algorithms that provide a framework for building 3D volumetric images of regions of moving anatomy using multiple fast multi-slice MRI studies. It is specifically motivated by the clinical application of unsedated fetal brain imaging, which has emerged as an important area for image analysis. The tool reads multiple DICOM image stacks acquired in any angulation into a consistent patient coordinate frame and allows the user to select regions to be locally motion corrected. It combines algorithms for slice motion estimation, bias field inconsistency correction and 3D volume reconstruction from multiple scattered slice stacks. The tool is built onto the RView (http://rview.colin-studholme.net) medical image display software and allows the user to inspect slice stacks, and apply both stack and slice level motion estimation that incorporates temporal constraints based on slice timing and interleave information read from the DICOM data. Following motion estimation an algorithm for bias field inconsistency correction provides the user with the ability to remove artifacts arising from the motion of the local anatomy relative to the imaging coils. Full 3D visualization of the slice stacks and individual slice orientations is provided to assist in evaluating the quality of the motion correction and final image reconstruction. The tool has been evaluated on a range of clinical data acquired on GE, Siemens and Philips MRI scanners.

Citation Download Citation

Kio Kim, Piotr A. Habas, Vidya Rajagopalan, Julia Scott, Francois Rousseau, A. James Barkovich, Orit A. Glenn, and Colin Studholme "SLIMMER: SLIce MRI motion estimation and reconstruction tool for studies of fetal anatomy", Proc. SPIE 7962, Medical Imaging 2011: Image Processing, 79624D (11 March 2011); https://doi.org/10.1117/12.878489

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