MR to CT registration of brains using image synthesis

Snehashis Roy, Aaron Carass, Amod Jog, Jerry L. Prince, Junghoon Lee

Research output: Chapter in Book/Report/Conference proceedingConference contribution

29 Scopus citations


Computed tomography (CT) is the preferred imaging modality for patient dose calculation for radiation therapy. Magnetic resonance (MR) imaging (MRI) is used along with CT to identify brain structures due to its superior soft tissue contrast. Registration of MR and CT is necessary for accurate delineation of the tumor and other structures, and is critical in radiotherapy planning. Mutual information (MI) or its variants are typically used as a similarity metric to register MRI to CT. However, unlike CT, MRI intensity does not have an accepted calibrated intensity scale. Therefore, MI-based MR-CT registration may vary from scan to scan as MI depends on the joint histogram of the images. In this paper, we propose a fully automatic framework for MR-CT registration by synthesizing a synthetic CT image from MRI using a co-registered pair of MR and CT images as an atlas. Patches of the subject MRI are matched to the atlas and the synthetic CT patches are estimated in a probabilistic framework. The synthetic CT is registered to the original CT using a deformable registration and the computed deformation is applied to the MRI. In contrast to most existing methods, we do not need any manual intervention such as picking landmarks or regions of interests. The proposed method was validated on ten brain cancer patient cases, showing 25% improvement in MI and correlation between MR and CT images after registration compared to state-of-the-art registration methods.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2014
Subtitle of host publicationImage Processing
ISBN (Print)9780819498274
StatePublished - 2014
EventMedical Imaging 2014: Image Processing - San Diego, CA, United States
Duration: Feb 16 2014Feb 18 2014

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


OtherMedical Imaging 2014: Image Processing
Country/TerritoryUnited States
CitySan Diego, CA


  • Brain
  • CT
  • Hallucination
  • Histogram matching
  • Image synthesis
  • Intensity normalization
  • MRI
  • Magnetic resonance imaging
  • Patches

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging


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