Anand A. Joshi

Surface-Constrained Volumetric Brain Registration Using Harmonic Mappings

In order to compare anatomical and functional brain imaging data across subjects, the images must first be registered to a common coordinate system in which anatomical features are aligned. Intensity-based volume registration methods can align subcortical structures well, but the variability in sulcal folding patterns typically results in misalignment of the cortical surface. Conversely, surface-based registration using sulcal features can produce excellent cortical alignment but the mapping between brains is restricted to the cortical surface. Here we describe a method for volumetric registration that also produces an accurate one-to-one point correspondence between cortical surfaces. This is achieved by first parameterizing and aligning the cortical surfaces using sulcal landmarks. We then use a constrained harmonic mapping to extend this surface correspondence to the entire cortical volume. Finally, this mapping is refined using an intensity-based warp. We demonstrate the utility of the method by applying it to T1-weighted magnetic resonance images (MRIs). We evaluate the performance of our proposed method relative to existing methods that use only intensity information; for this comparison we compute the intersubject alignment of expert-labeled subcortical structures after registration.

Resting-state fMRI can reliably map neural networks in children

Resting-state MRI (rs-fMRI) is a powerful procedure for studying whole-brain neural connectivity. In this study we provide the first empirical evidence of the longitudinal reliability of rs-fMRI in children. We compared rest-retest measurements across spatial, temporal and frequency domains for each of six cognitive and sensorimotor intrinsic connectivity networks (ICNs) both within and between scan sessions. Using KendallsW, concordance of spatial maps ranged from .60 to .86 across networks, for various derived measures. The Pearson correlation coefficient for temporal coherence between networks across all Time 1-Time 2 (T1/T2) z-converted measures was .66 (p<.001). There were no differences between T1/T2 measurements in low-frequency power of the ICNs. For the visual network, within-session T1 correlated with the T2 low-frequency power, across participants. These measures from resting-state data in children were consistent across multiple domains (spatial, temporal, and frequency). Resting-state connectivity is therefore a reliable method for assessing large-scale brain networks in children.

Comparison of landmark-based and automatic methods for cortical surface registration

Group analysis of structure or function in cerebral cortex typically involves, as a first step, the alignment of cortices. A surface-based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages FreeSurfer and BrainVoyager. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for ROIs in the perisylvian region for the landmark-based method and FreeSurfer. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis.

The contribution of genes to cortical thickness and volume.

We analyzed brain MRI data from 372 young adult twins toidentify cortical regions in which gray matter thickness and volume are influenced by genetics. This was achieved using an A/C/E structural equation model that divides the variance of these traits, at each point on the cortex, into additive genetic (A), shared (C), and unique environmental (E) components. A strong genetic influencewas found in frontal and parietal regions. Inaddition, we correlated cortical thickness with full-scale intelligence quotient for comparison with the A/C/E maps, and several regions where cortical structure was correlated with intelligence quotient are under genetic control. These cortical measures may be useful phenotypes to narrow the searchfor quantitative trait lociinfluencing brain structure.

Illumination pattern optimization for fluorescence tomography: theory and simulation studies.

Fluorescence molecular tomography is a powerful tool for 3D visualization of molecular targets and pathways in vivo in small animals. Owing to the high degrees of absorption and scattering of light through tissue, the fluorescence tomographic inverse problem is inherently ill-posed. In order to improve source localization and the conditioning of the light propagation model, multiple sets of data are acquired by illuminating the animal surface with different spatial patterns of near-infrared light. However, the choice of these patterns in most experimental setups is ad hoc and suboptimal. This paper presents a systematic approach for designing efficient illumination patterns for fluorescence tomography. Our objective here is to determine how to optimally illuminate the animal surface so as to maximize the information content in the acquired data. We achieve this by improving the conditioning of the Fisher information matrix. We parameterize the spatial illumination patterns and formulate our problem as a constrained optimization problem that, for a fixed number of illumination patterns, yields the optimal set of patterns. For geometric insight, we used our method to generate a set of three optimal patterns for an optically homogeneous, regular geometrical shape and observed expected symmetries in the result. We also generated a set of six optimal patterns for an optically homogeneous cuboidal phantom set up in the transillumination mode. Finally, we computed optimal illumination patterns for an optically inhomogeneous realistically shaped mouse atlas for different given numbers of patterns. The regularized pseudoinverse matrix, generated using the singular value decomposition, was employed to reconstruct the point spread function for each set of patterns in the presence of a sample fluorescent point source deep inside the mouse atlas. We have evaluated the performance of our method by examining the singular value spectra as well as plots of average spatial resolution versus estimator variance corresponding to different illumination schemes.

Automatic intra-subject registration-based segmentation of abdominal fat from water–fat MRI

To develop an automatic registration‐based segmentation algorithm for measuring abdominal adipose tissue depot volumes and organ fat fraction content from three‐dimensional (3D) water–fat MRI data, and to evaluate its performance against manual segmentation.

High-resolution 18F-FDG PET with MRI for monitoring response to treatment in rheumatoid arthritis

Eur J Nucl Med Mol Imaging (2010) 37:1047 DOI 10.1007/s00259-009-1364-x IMAGE OF THE MONTH High-resolution 18 F-FDG PET with MRI for monitoring response to treatment in rheumatoid arthritis Abhijit J. Chaudhari & Spencer L. Bowen & George W. Burkett & Nathan J. Packard & Felipe Godinez & Anand A. Joshi & Stanley M. Naguwa & David K. Shelton & John C. Hunter & John M. Boone & Michael H. Buonocore & Ramsey D. Badawi Received: 20 November 2009 / Accepted: 10 December 2009 / Published online: 30 January 2010 # The Author(s) 2010. This article is published with open access at Springerlink.com Molecular imaging can potentially provide means for mon- itoring response to therapy in rheumatoid arthritis (RA) early in the course of disease [1].Quantitative measurements of RA disease activity made in the wrist by whole-body PET scanners, however, have inadequate accuracy because of limited spatial resolution [2]. A high-resolution PET/CT scanner for imaging extremities has been built at our insti- tution [3]. In conjunction with a clinical MRI scanner, high- resolution PET/MR images can be obtained for the wrist. The CT image is used for PET/MR image coregistration. A 57-year-old female with established RA was stable until a recent clinical flare-up in the right wrist. Clinical exami- nation revealed synovitis, swelling, and diminished range of motion. The patient also had a history of osteoarthritis (OA). An extremity 18 F-FDG PET/CT scan immediately following MRI at baseline was performed on this patient. Tumor necrosis factor alpha (TNF-α) inhibitor (etanercept) therapy was then initiated as a part of the patient’s standard of care. The patient was re-scanned 5 weeks after starting treatment. The figure shows high-resolution 18 F-FDG PET images (pseudocolor) overlaid on pre-contrast MRI images (gray This work was funded by the NIH grants UL1-RR024146, R01CA129561, R01EB002138 and the UC Davis Imaging Research Center. A. J. Chaudhari (*) : S. L. Bowen : G. W. Burkett : N. J. Packard : F. Godinez : D. K. Shelton : J. C. Hunter : J. M. Boone : M. H. Buonocore : R. D. Badawi Department of Radiology, UC Davis Medical Center, Sacramento, CA, USA e-mail: ajchaudhari@ucdavis.edu A. A. Joshi Department of Neurology, UCLA School of Medicine, Los Angeles, CA, USA S. M. Naguwa Department of Internal Medicine, UC Davis Medical Center, Sacramento, CA, USA scale) at baseline (left column) and 5 weeks (right column). Significant reduction in PET signal (suggesting reduced inflammation) in the synovium and at sites of erosions (white arrows) is visible. The green arrow shows inflammation due to OA. Physician examination at 3 months confirmed that this patient responded positively to etanercept. This case illustrates the potential of high-resolution PET with MRI for quantitative visualization of early response to therapy in RA. Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which per- mits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. References 1. Brenner W. 18F-FDG PET in rheumatoid arthritis: there still is a long way to go. J Nucl Med. 2004;45(6):927–9. 2. Beckers C, Ribbens C, Andre B, Marcelis S, Kaye O, Mathy L, et al. Assessment of disease activity in rheumatoid arthritis with (18)F-FDG PET. J Nucl Med. 2004;45(6):956–64. 3. Bowen SL, Wu Y, Chaudhari AJ, Fu L, Packard NJ, Burkett GW, et al. Initial characterization of a dedicated breast PET/CT scanner during human imaging. J Nucl Med. 2009;50(9):1401–8.

Sex differences in the human connectome: 4-Tesla high angular resolution diffusion imaging (HARDI) tractography in 234 young adult twins

Cortical connectivity is associated with cognitive and behavioral traits that are thought to vary between sexes. Using high-angular resolution diffusion imaging at 4 Tesla, we scanned 234 young adult twins and siblings (mean age: 23.4 ± 2.0 SD years) with 94 diffusion-encoding directions. We applied a novel Hough transform method to extract fiber tracts throughout the entire brain, based on fields of constant solid angle orientation distribution functions (ODFs). Cortical surfaces were generated from each subjects 3D T1-weighted structural MRI scan, and tracts were aligned to the anatomy. Network analysis revealed the proportions of fibers interconnecting 5 key subregions of the frontal cortex, including connections between hemispheres. We found significant sex differences (147 women/87 men) in the proportions of fibers connecting contralateral superior frontal cortices. Interhemispheric connectivity was greater in women, in line with long-standing theories of hemispheric specialization. These findings may be relevant for ongoing studies of the human connectome.

Cortical surface parameterization by p-harmonic energy minimization

Cortical surface parameterization has several applications in visualization and analysis of the brain surface. Here we propose a scheme for parameterizing the surface of the cerebral cortex. The parameterization is formulated as the minimization of an energy functional in the p/sup th/ norm. A numerical method for obtaining the solution is also presented. Brain surfaces from multiple subjects are brought into common parameter space using the scheme. 3D spatial averages of the cortical surfaces are generated by using the correspondences induced by common parameter space.

Semi-automated method for delineation of landmarks on models of the cerebral cortex.

Sulcal and gyral landmarks on the human cerebral cortex are required for various studies of the human brain. Whether used directly to examine sulcal geometry, or indirectly to drive cortical surface registration methods, the accuracy of these landmarks is essential. While several methods have been developed to automatically identify sulci and gyri, their accuracy may be insufficient for certain neuroanatomical studies. We describe a semi-automated procedure that delineates a sulcus or gyrus given a limited number of user-selected points. The method uses a graph theory approach to identify the lowest-cost path between the points, where the cost is a combination of local curvature features and the distance between vertices on the surface representation. We implemented the algorithm in an interface that guides the user through a cortical surface delineation protocol, and we incorporated this tool into our BrainSuite software. We performed a study to compare the results produced using our method with results produced using Display, a popular tool that has been used extensively for manual delineation of sulcal landmarks. Six raters were trained on the delineation protocol. They performed delineations on 12 brains using both software packages. We performed a statistical analysis of 3 aspects of the delineation task: time required to delineate the surface, registration accuracy achieved compared to an expert-delineated gold-standard, and variation among raters. Our new method was shown to be faster to use, to provide reduced inter-rater variability, and to provide results that were at least as accurate as those produced using Display.