2D-3D Rigid-Body Registration of X-Ray Fluoroscopy and CT Images

The registration of pre-operative volumetric datasets to intra- operative two-dimensional images provides an improved way of verifying patient position and medical instrument loca- tion. In applications from orthopedics to neurosurgery, it has a great value in maintaining up-to-date information about changes due to intervention. We propose a mutual information- based registration algorithm to establish the proper align- ment. For optimization purposes, we compare the perfor- mance of the non-gradient Powell method and two slightly di erent versions of a stochastic gradient ascent strategy: one using a sparsely sampled histogramming approach and the other Parzen windowing to carry out probability density approximation. Our main contribution lies in adopting the stochastic ap- proximation scheme successfully applied in 3D-3D registra- tion problems to the 2D-3D scenario, which obviates the need for the generation of full DRRs at each iteration of pose op- timization. This facilitates a considerable savings in compu- tation expense. We also introduce a new probability density estimator for image intensities via sparse histogramming, de- rive gradient estimates for the density measures required by the maximization procedure and introduce the framework for a multiresolution strategy to the problem. Registration results are presented on uoroscopy and CT datasets of a plastic pelvis and a real skull, and on a high-resolution CT- derived simulated dataset of a real skull, a plastic skull, a plastic pelvis and a plastic lumbar spine segment

A Unified Statistical and Information Theoretic Framework for Multi-modal Image Registration

We formulate and interpret several multi-modal registration methods in the context of a unified statistical and information theoretic framework. A unified interpretation clarifies the implicit assumptions of each method yielding a better understanding of their relative strengths and weaknesses. Additionally, we discuss a generative statistical model from which we derive a novel analysis tool, the "auto-information function", as a means of assessing and exploiting the common spatial dependencies inherent in multi-modal imagery. We analytically derive useful properties of the "auto-information" as well as verify them empirically on multi-modal imagery. Among the useful aspects of the "auto-information function" is that it can be computed from imaging modalities independently and it allows one to decompose the search space of registration problems

A combined fMRI and DTI examination of functional language lateralization and arcuate fasciculus structure: Effects of degree versus direction of hand preference Author links open overlay panel

The present study examined the relationship between hand preference degree and direction, functional language lateralization in Broca’s and Wernicke’s areas, and structural measures of the arcuate fasciculus. Results revealed an effect of degree of hand preference on arcuate fasciculus structure, such that consistently-handed individuals, regardless of the direction of hand preference, demonstrated the most asymmetric arcuate fasciculus, with larger left versus right arcuate, as measured by DTI. Functional language lateralization in Wernicke’s area, measured via fMRI, was related to arcuate fasciculus volume in consistent-left-handers only, and only in people who were not right hemisphere lateralized for language; given the small sample size for this finding, the future investigation is warranted. Results suggest handedness degree may be an important variable to investigate in the context of neuroanatomical asymmetries

A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0-2 year age range

We present a detailed description of a set of FreeSurfer compatible segmentation guidelines tailored to infant MRI scans, and a unique data set of manually segmented acquisitions, with subjects nearly evenly distributed between 0 and 2 years of age. We believe that these segmentation guidelines and this dataset will have a wide range of potential uses in medicine and neuroscience.Eunice Kennedy Shriver National Institute of Child Health and Human Development (U.S.) (Grant 1K99HD061485-01A1)Eunice Kennedy Shriver National Institute of Child Health and Human Development (U.S.) (Grant R00 HD061485-03)Ralph Schlaeger FellowshipNational Institutes of Health (U.S.) (1R01EB014947-01)National Institutes of Health (U.S.) (K23 NS42758-01)National Center for Research Resources (U.S.) (P41-RR14075)National Center for Research Resources (U.S.) (U24 RR021382)National Institutes of Health. National Institute for Biomedical Imaging and Bioengineering (R01EB006758)National Institute on Aging (AG022381)National Institute on Aging (5R01AG008122-22)National Institute of Neurological Disorders and Stroke (U.S.) (R01 NS052585-01)National Institute of Neurological Disorders and Stroke (U.S.) (1R21NS072652-01)National Institute of Neurological Disorders and Stroke (U.S.) (1R01NS070963)National Center for Research Resources (U.S.) (Shared Instrumentation Grant 1S10RR023401)National Center for Research Resources (U.S.) (Shared Instrumentation Grant 1S10RR019307)National Center for Research Resources (U.S.) (Shared Instrumentation Grant 1S10RR023043)Ellison Medical FoundationNational Institutes of Health. Blueprint for Neuroscience Research (5U01-MH093765)Human Connectome Projec

Efficient Population Registration of 3D Data

We present a population registration framework that acts on large collections or populations of data volumes. The data alignment procedure runs in a simultaneous fashion, with every member of the population approaching the central tendency of the collection at the same time. Such a mechanism eliminates the need for selecting a particular reference frame a priori, resulting in a non-biased estimate of a digital atlas. Our algorithm adopts an affine congealing framework with an information theoretic objective function and is optimized via a gradientbased stochastic approximation process embedded in a multi-resolution setting. We present experimental results on both synthetic and real images

A Unified Information Theoretic Framework for Pair- and Group-wise Registration of Medical Images

PhD thesisThe field of medical image analysis has been rapidly growing for the past two decades. Besides a significant growth in computational power, scanner performance, and storage facilities, this acceleration is partially due to an unprecedented increase in the amount of data sets accessible for researchers. Medical experts traditionally rely on manual comparisons of images, but the abundance of information now available makes this task increasingly difficult. Such a challenge prompts for more automation in processing the images.In order to carry out any sort of comparison among multiple medical images, onefrequently needs to identify the proper correspondence between them. This step allows us to follow the changes that happen to anatomy throughout a time interval, to identify differences between individuals, or to acquire complementary information from different data modalities. Registration achieves such a correspondence. In this dissertation we focus on the unified analysis and characterization of statistical registration approaches.We formulate and interpret a select group of pair-wise registration methods in the context of a unified statistical and information theoretic framework. This clarifies the implicit assumptions of each method and yields a better understanding of their relative strengths and weaknesses. This guides us to a new registration algorithm that incorporates the advantages of the previously described methods. Next we extend the unified formulation with analysis of the group-wise registration algorithms that align a population as opposed to pairs of data sets. Finally, we present our group-wise registration framework, stochastic congealing. The algorithm runs in a simultaneous fashion, with every member of the population approaching the central tendency of the collection at the same time. It eliminates the need for selecting a particular referenceframe a priori, resulting in a non-biased estimate of a digital template. Our algorithm adopts an information theoretic objective function which is optimized via a gradientbased stochastic approximation process embedded in a multi-resolution setting. We demonstrate the accuracy and performance characteristics of stochastic congealing via experiments on both synthetic and real images

Anatomical priors for global probabilistic diffusion tractography

We investigate the use of anatomical priors in a Bayesian framework for diffusion tractography. We compare priors that utilize different types of information on the white-matter pathways to be reconstructed. This information includes manually labeled paths from a set of training subjects and anatomical segmentation labels obtained from T1-weighted MR images of the same subjects. Our results indicate that the use of prior information increases robustness to end-point ROI size and yields solutions that agree with expert-drawn manual labels, obviating the need for manual intervention on any new test subjects.National Institute of Biomedical Imaging and Bioengineering (U.S.) (K99/R00 Pathway to Independence Award EB008129)National Institute of Biomedical Imaging and Bioengineering (U.S.) (Grant R01-EB001550)National Institute of Biomedical Imaging and Bioengineering (U.S.) (Grant R01-EB006758)National Center for Research Resources (U.S.) (Grant P41-RR14075)National Center for Research Resources (U.S.) (Grant R01-RR16594)National Center for Research Resources (U.S.) (NCRR BIRN Morphometric Project BIRN002 Grant U24-RR0213820)National Institute of Neurological Disorders and Stroke (U.S.) (Grant R01-NS052585)Mind Research InstituteNational Alliance for Medical Image Computing (U.S.) the MIND Institute, and the National Alliance for Medical Image Computing (NIH Roadmap for Medical Research Grant U54-EB005149

Multimodal Whole Brain Registration: MRI and High Resolution Histology

Three-dimensional brain imaging through cutting-edge MRI technology allows assessment of physical and chemical tissue properties at sub-millimeter resolution. In order to improve brain understanding as part of diagnostic tasks using MRI images, other imaging modalities to obtain deep cerebral structures and cytoarchitectural boundaries have been investigated. Under availability of postmortem samples, the fusion of MRI to brain histology supports more accurate description of neuroanatomical structures since it preserves microscopic entities and reveal fine anatomical details, unavailable otherwise. Nonetheless, histological processing causes severe tissue deformation and loss of the brain original 3D conformation, preventing direct comparisons between MRI and histology. This paper proposes an interactive computational pipeline designed to register multimodal brain data and enable direct histology-MRI correlation. Our main contribution is to develop schemes for brain data fusion, distortion corrections, using appropriate diffeomorphic mappings to align the 3D histological and MRI volumes. We describe our pipeline and preliminary developments of scalable processing schemes for highresolution images. Tests consider a postmortem human brain, and include qualitatively and quantitatively results, such as 3D visualizations and the Dice coefficient (DC) between brain structures. Preliminary results show promising DC values when comparing our scheme results to manually labeled neuroanatomical regions defined by a neurosurgeon on MRI and histology data sets. DC was computed for the left caudade gyrus (LC), right hippocampus (RH) and lateral ventricles (LV)

Reorganization of the somatosensory cortex in hemiplegic cerebral palsy associated with impaired sensory tracts

Functional neuroimaging studies argue that sensory deficits in hemiplegic cerebral palsy (HCP) are related to deviant somatosensory processing in the ipsilesional primary somatosensory cortex (S1). A separate body of structural neuroimaging literature argues that these deficits are due to structural damage of the ascending sensory tracts (AST). The relationship between the functional and structural integrity of the somatosensory system and the sensory performance is largely unknown in HCP. To address this relationship, we combined findings from magnetoencephalography (MEG) and probabilistic diffusion tractography (PDT) in 10 children with HCP and 13 typically developing (TD) children. With MEG, we mapped the functionally active regions in the contralateral S1 during tactile stimulation of the thumb, middle, and little fingers of both hands. Using these MEG-defined functional active regions as regions of interest for PDT, we estimated the diffusion parameters of the AST. Somatosensory function was assessed via two-point discrimination tests. Our MEG data showed: (i) an abnormal somatotopic organization in all children with HCP in either one or both of their hemispheres; (ii) longer Euclidean distances between the digit maps in the S1 of children with HCP compared to TD children; (iii) suppressed gamma responses at early latencies for both hemispheres of children with HCP; and (iv) a positive correlation between the Euclidean distances and the sensory tests for the more affected hemisphere of children with HCP. Our MEG-guided PDT data showed: (i) higher mean and radian diffusivity of the AST in children with HCP; (ii) a positive correlation between the axial diffusivity of the AST with the sensory tests for the more affected hemisphere; and (iii) a negative correlation between the gamma power change and the AD of the AST for the MA hemisphere. Our findings associate for the first time bilateral cortical functional reorganization in the S1 of HCP children with abnormalities in the structural integrity of the AST, and correlate these abnormalities with behaviorally-assessed sensory deficits