M. Faisal Beg

Bio: M. Faisal Beg is an academic researcher from Simon Fraser University. The author has contributed to research in topics: Large deformation diffeomorphic metric mapping & Computational anatomy. The author has an hindex of 7, co-authored 10 publications receiving 1713 citations. Previous affiliations of M. Faisal Beg include Johns Hopkins University.

Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms

Abstract: This paper examine the Euler-Lagrange equations for the solution of the large deformation diffeomorphic metric mapping problem studied in Dupuis et al. (1998) and Trouve (1995) in which two images I 0, I 1 are given and connected via the diffeomorphic change of coordinates I 0???1=I 1 where ?=?1 is the end point at t= 1 of curve ? t , t?[0, 1] satisfying .? t =v t (? t ), t? [0,1] with ?0=id. The variational problem takes the form $$\mathop {\arg {\text{m}}in}\limits_{\upsilon :\dot \phi _t = \upsilon _t \left( {\dot \phi } \right)} \left( {\int_0^1 {\left\| {\upsilon _t } \right\|} ^2 {\text{d}}t + \left\| {I_0 \circ \phi _1^{ - 1} - I_1 } \right\|_{L^2 }^2 } \right),$$ where ?v t? V is an appropriate Sobolev norm on the velocity field v t(·), and the second term enforces matching of the images with ?·?L 2 representing the squared-error norm. In this paper we derive the Euler-Lagrange equations characterizing the minimizing vector fields v t, t?[0, 1] assuming sufficient smoothness of the norm to guarantee existence of solutions in the space of diffeomorphisms. We describe the implementation of the Euler equations using semi-lagrangian method of computing particle flows and show the solutions for various examples. As well, we compute the metric distance on several anatomical configurations as measured by ?0 1?v t? V dt on the geodesic shortest paths.

Increasing the power of functional maps of the medial temporal lobe by using large deformation diffeomorphic metric mapping

Abstract: The functional magnetic resonance imagery responses of declarative memory tasks in the medial temporal lobe (MTL) are examined by using large deformation diffeomorphic metric mapping (LDDMM) to remove anatomical variations across subjects. LDDMM is used to map the structures of the MTL in multiple subjects into extrinsic atlas coordinates; these same diffeomorphic mappings are used to transfer the corresponding functional data activation to the same extrinsic coordinates. The statistical power in the averaged LDDMM mapped signals is significantly increased over conventional Talairach–Tournoux averaging. Activation patterns are highly localized within the MTL. Whereas the present demonstration has been aimed at enhancing alignment within the MTL, this technique is general and can be applied throughout the brain.

Fully-automated, multi-stage hippocampus mapping in very mild Alzheimer disease.

Abstract: Landmark-based high-dimensional diffeomorphic maps of the hippocampus (although accurate) is highly-dependent on rater’s anatomic knowledge of the hippocampus in the magnetic resonance images. It is therefore vulnerable to rater drift and errors if substantial amount of effort is not spent on quality assurance, training, and re-training. A fully-automated, FreeSurfer-initialized large-deformation diffeomorphic metric mapping procedure of small brain substructures, including the hippocampus, has been previously developed and validated in small samples. In this report, we demonstrate that this fully-automated pipeline can be used in place of the landmark-based procedure in a large-sample clinical study to produce similar statistical outcomes. Some direct comparisons of the two procedures are also presented.

Hippocampal surface mapping of genetic risk factors in AD via sparse learning models

Abstract: Genetic mapping of hippocampal shape, an under-explored area, has strong potential as a neurodegeneration biomarker for AD and MCI. This study investigates the genetic effects of top candidate single nucleotide polymorphisms (SNPs) on hippocampal shape features as quantitative traits (QTs) in a large cohort. FS+LDDMM was used to segment hippocampal surfaces from MRI scans and shape features were extracted after surface registration. Elastic net (EN) and sparse canonical correlation analysis (SCCA) were proposed to examine SNP-QT associations, and compared with multiple regression (MR). Although similar in power, EN yielded substantially fewer predictors than MR. Detailed surface mapping of global and localized genetic effects were identified by MR and EN to reveal multi-SNP-single-QT relationships, and by SCCA to discover multi-SNP-multi-QT associations. Shape analysis identified stronger SNP-QT correlations than volume analysis. Sparse multivariate models have greater power to reveal complex SNP-QT relationships. Genetic analysis of quantitative shape features has considerable potential for enhancing mechanistic understanding of complex disorders like AD.

elastix : A Toolbox for Intensity-Based Medical Image Registration

Abstract: Medical image registration is an important task in medical image processing. It refers to the process of aligning data sets, possibly from different modalities (e.g., magnetic resonance and computed tomography), different time points (e.g., follow-up scans), and/or different subjects (in case of population studies). A large number of methods for image registration are described in the literature. Unfortunately, there is not one method that works for all applications. We have therefore developed elastix, a publicly available computer program for intensity-based medical image registration. The software consists of a collection of algorithms that are commonly used to solve medical image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. The command-line interface enables automated processing of large numbers of data sets, by means of scripting. The usage of elastix for comparing different registration methods is illustrated with three example experiments, in which individual components of the registration method are varied.