Slide 1
An Anatomically Curated Fiber Clustering White Matter Atlas for Consistent White Matter Tract Parcellation across the Lifespan
Slide 2
An Immersive Virtual Reality Environment for Diagnostic Imaging
Slide 3
Inter-site and Inter-scanner Diffusion MRI Data Harmonization
Slide 4
The Open Anatomy Browser: A Collaborative Web-Based Viewer for Interoperable Anatomy Atlases
Slide 5
Unsupervised Discovery of Emphysema Subtypes in a Large Clinical Cohort
Slide 6
Identifying Shared Brain Networks in Individuals by Decoupling Functional and Anatomical Variability
Slide 7
Supra-Threshold Fiber Cluster Statistics for Data-Driven Whole Brain Tractography Analysis
Slide 8
Free Water Modeling of Peritumoral Edema using Multi-fiber Tractography
Slide 8
Estimation of Bounded and Unbounded Trajectories in Diffusion MRI
Slide 9
Principal Gradient of Macroscale Cortical Organization
Slide 10
Evolution of a Simultaneous Segmentation and Atlas Registration
Slide 11
Multi-modality MRI-based Atlas of the Brain
Slide 12
Intracranial Fluid Redistribution
Slide 13
Corticospinal Tract Modeling for Neurosurgical Planning by Tracking through Regions of Peritumoral Edema and Crossing Fibers
Slide 14
Automated White Matter Fiber Tract Identification in Patients with Brain Tumors
Slide 15
State-space Models of Mental Processes from fMRI
Slide 16
Robust Initialization of Active Shape Models for Lung Segmentation in CT Scans: A Feature-Based Atlas Approach
Slide 17
Tractography-driven Groupwise Multi-Scale Parcellation of the Cortex
Slide 18
Gray Matter Alterations in Early Aging
Slide 19
Statistical Shape Analysis: From Landmarks to Diffeomorphisms
Slide 20
A Generative Probabilistic Model and Discriminative Extensions for Brain Lesion Segmentation
Slide 21
Joint Modeling of Imaging and Genetic Variability
Slide 22
MR-Ultrasound Fusion for Neurosurgery
Slide 23
Diffusion MRI and Tumor Heterogeneity
Slide 24
SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research

Neuroimage Analysis Center


The Neuroimaging Analysis Center is a research and technology center with the mission of advancing the role of neuroimaging in health care. The ability to access huge cohorts of patient medical records and radiology data, the emergence of ever-more detailed imaging modalities, and the availability of unprecedented computer processing power marks the possibility for a new era in neuroimaging, disease understanding, and patient treatment. We are excited to present a national resource center with the goal of finding new ways of extracting disease characteristics from advanced imaging and computation, and to make these methods available to the larger medical community through a proven methodology of world-class research, open-source software, and extensive collaboration.

Our Sponsor



The NAC is a Biomedical Technology Resource Center supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) (P41 EB015902). It was supported by the National Center for Research Resources (NCRR) (P41 RR13218) through December 2011.

Contact the Center Directors



Carl-Fredrik Westin, PhD
Laboratory of Mathematics in Imaging
Brigham and Women's Hospital
1249 Boylston St., Room 240
Boston, MA 02215
Phone: +1 617 525-6209
E-mail: westin at

Ron Kikinis

Ron Kikinis, MD
Surgical Planning Laboratory 
Brigham and Women's Hospital 
75 Francis St, L1 Room 050
Boston, MA 02115
Phone: +1 617 732-7389
E-mail: kikinis at


Recent Publications

  • Archip N, Clatz O, Whalen S, Kacher D, Fedorov A, Kot A, Chrisochoides N, Jolesz FA, Golby A, Black PM, Warfield SK. Non-rigid Alignment of Pre-operative MRI, fMRI, and DT-MRI with Intra-operative MRI for Enhanced Visualization and Navigation in Image-guided Neurosurgery. Neuroimage 2007;35(2):609-24.
    OBJECTIVE: The usefulness of neurosurgical navigation with current visualizations is seriously compromised by brain shift, which inevitably occurs during the course of the operation, significantly degrading the precise alignment between the pre-operative MR data and the intra-operative shape of the brain. Our objectives were (i) to evaluate the feasibility of non-rigid registration that compensates for the brain deformations within the time constraints imposed by neurosurgery, and (ii) to create augmented reality visualizations of critical structural and functional brain regions during neurosurgery using pre-operatively acquired fMRI and DT-MRI. MATERIALS AND METHODS: Eleven consecutive patients with supratentorial gliomas were included in our study. All underwent surgery at our intra-operative MR imaging-guided therapy facility and have tumors in eloquent brain areas (e.g. precentral gyrus and cortico-spinal tract). Functional MRI and DT-MRI, together with MPRAGE and T2w structural MRI were acquired at 3 T prior to surgery. SPGR and T2w images were acquired with a 0.5 T magnet during each procedure. Quantitative assessment of the alignment accuracy was carried out and compared with current state-of-the-art systems based only on rigid registration. RESULTS: Alignment between pre-operative and intra-operative datasets was successfully carried out during surgery for all patients. Overall, the mean residual displacement remaining after non-rigid registration was 1.82 mm. There is a statistically significant improvement in alignment accuracy utilizing our non-rigid registration in comparison to the currently used technology (p<0.001). CONCLUSIONS: We were able to achieve intra-operative rigid and non-rigid registration of (1) pre-operative structural MRI with intra-operative T1w MRI; (2) pre-operative fMRI with intra-operative T1w MRI, and (3) pre-operative DT-MRI with intra-operative T1w MRI. The registration algorithms as implemented were sufficiently robust and rapid to meet the hard real-time constraints of intra-operative surgical decision making. The validation experiments demonstrate that we can accurately compensate for the deformation of the brain and thus can construct an augmented reality visualization to aid the surgeon.
  • Alayón S, Robertson R, Warfield SK, Ruiz-Alzola J. A fuzzy system for helping medical diagnosis of malformations of cortical development. J Biomed Inform 2007;40(3):221-35.
    Malformations of the cerebral cortex are recognized as a common cause of developmental delay, neurological deficits, mental retardation and epilepsy. Currently, the diagnosis of cerebral cortical malformations is based on a subjective interpretation of neuroimaging characteristics of the cerebral gray matter and underlying white matter. There is no automated system for aiding the observer in making the diagnosis of a cortical malformation. In this paper a fuzzy rule-based system is proposed as a solution for this problem. The system collects the available expert knowledge about cortical malformations and assists the medical observer in arriving at a correct diagnosis. Moreover, the system allows the study of the influence of the various factors that take part in the decision. The evaluation of the system has been carried out by comparing the automated diagnostic algorithm with known case examples of various malformations due to abnormal cortical organization. An exhaustive evaluation of the system by comparison with published cases and a ROC analysis is presented in the paper.
  • Melonakos J, Niethammer M, Mohan V, Kubicki M, Miller J, Tannenbaum A. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Proc IEEE Int Conf Comput Vis 2007;:1-8.
    In this paper, we describe a method for segmenting fiber bundles from diffusion-weighted magnetic resonance images using a locally-constrained region based approach. From a pre-computed optimal path, the algorithm propagates outward capturing only those voxels which are locally connected to the fiber bundle. Rather than attempting to find large numbers of open curves or single fibers, which individually have questionable meaning, this method segments the full fiber bundle region. The strengths of this approach include its ease-of-use, computational speed, and applicability to a wide range of fiber bundles. In this work, we show results for segmenting the cingulum bundle. Finally, we explain how this approach and extensions thereto overcome a major problem that typical region-based flows experience when attempting to segment neural fiber bundles.
  • Brem MH, Pauser J, Yoshioka H, Brenning A, Stratmann J, Hennig FF, Kikinis R, Duryea J, Winalski CS, Lang P. Longitudinal in vivo reproducibility of cartilage volume and surface in osteoarthritis of the knee. Skeletal Radiol 2007;36(4):315-20.
    OBJECTIVE: The aim of this study was to evaluate the longitudinal reproducibility of cartilage volume and surface area measurements in moderate osteoarthritis (OA) of the knee.
  • Lashkari D, Golland P. Convex Clustering with Exemplar-Based Models. Adv Neural Inf Process Syst 2007;20
    Clustering is often formulated as the maximum likelihood estimation of a mixture model that explains the data. The EM algorithm widely used to solve the resulting optimization problem is inherently a gradient-descent method and is sensitive to initialization. The resulting solution is a local optimum in the neighborhood of the initial guess. This sensitivity to initialization presents a significant challenge in clustering large data sets into many clusters. In this paper, we present a different approach to approximate mixture fitting for clustering. We introduce an exemplar-based likelihood function that approximates the exact likelihood. This formulation leads to a convex minimization problem and an efficient algorithm with guaranteed convergence to the globally optimal solution. The resulting clustering can be thought of as a probabilistic mapping of the data points to the set of exemplars that minimizes the average distance and the information-theoretic cost of mapping. We present experimental results illustrating the performance of our algorithm and its comparison with the conventional approach to mixture model clustering.