title: Patch Based Synthesis of Whole Head MR Images: Application to EPI Distortion Correction.
abstract: Different magnetic resonance imaging pulse sequences are used to generate image contrasts based on physical properties of tissues, which provide different and often complementary information about them. Therefore multiple image contrasts are useful for multimodal analysis of medical images. Often, medical image processing algorithms are optimized for particular image contrasts. If a desirable contrast is unavailable, contrast synthesis (or modality synthesis) methods try to "synthesize" the unavailable constrasts from the available ones. Most of the recent image synthesis methods generate synthetic brain images, while whole head magnetic resonance (MR) images can also be useful for many applications. We propose an atlas based patch matching algorithm to synthesizeT2-w whole head (including brain, skull, eyes etc) images fromT1-w images for the purpose of distortion correction of diffusion weighted MR images. The geometric distortion in diffusion MR images due to in-homogeneousB0magnetic field are often corrected by non-linearly registering the correspondingb= 0 image with zero diffusion gradient to an undistortedT2-w image. We show that our syntheticT2-w images can be used as a template in absence of a realT2-w image. Our patch based method requires multiple atlases withT1andT2to be registeLowRes to a given targetT1. Then for every patch on the target, multiple similar looking matching patches are found on the atlasT1images and corresponding patches on the atlasT2images are combined to generate a syntheticT2of the target. We experimented on image data obtained from 44 patients with traumatic brain injury (TBI), and showed that our synthesizedT2images produce more accurate distortion correction than a state-of-the-art registration based image synthesis method.
authors.affiliation: Center for Neuroscience and Regenerative Medicine, Henry Jackson Foundation.
authors.forename: Snehashis
authors.initials: S
authors.lastname: Roy
authors.affiliation: Center for Neuroscience and Regenerative Medicine, Henry Jackson Foundation.
authors.forename: Yi-Yu
authors.initials: YY
authors.lastname: Chou
authors.affiliation: Department of Computer Science, The Johns Hopkins University.
authors.forename: Amod
authors.initials: A
authors.lastname: Jog
authors.affiliation: Diagnostic Radiology Department, National Institute of Health.
authors.forename: John A
authors.initials: JA
authors.lastname: Butman
authors.affiliation: Center for Neuroscience and Regenerative Medicine, Henry Jackson Foundation.
authors.forename: Dzung L
authors.initials: DL
authors.lastname: Pham
keywords: EPI; distortion correction; image synthesis; patches