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

  • Verhey JF, Wisser J, Warfield SK, Rexilius J, Kikinis R. Non-rigid registration of a 3D ultrasound and a MR image data set of the female pelvic floor using a biomechanical model. Biomed Eng Online. 2005;4:19.
    BACKGROUND: The visual combination of different modalities is essential for many medical imaging applications in the field of Computer-Assisted medical Diagnosis (CAD) to enhance the clinical information content. Clinically, incontinence is a diagnosis with high clinical prevalence and morbidity rate. The search for a method to identify risk patients and to control the success of operations is still a challenging task. The conjunction of magnetic resonance (MR) and 3D ultrasound (US) image data sets could lead to a new clinical visual representation of the morphology as we show with corresponding data sets of the female anal canal with this paper. METHODS: We present a feasibility study for a non-rigid registration technique based on a biomechanical model for MR and US image data sets of the female anal canal as a base for a new innovative clinical visual representation. RESULTS: It is shown in this case study that the internal and external sphincter region could be registered elastically and the registration partially corrects the compression induced by the ultrasound transducer, so the MR data set showing the native anatomy is used as a frame for the US data set showing the same region with higher resolution but distorted by the transducer CONCLUSION: The morphology is of special interest in the assessment of anal incontinence and the non-rigid registration of normal clinical MR and US image data sets is a new field of the adaptation of this method incorporating the advantages of both technologies.
  • Friman O, Westin CF. Resampling fMRI time series. Neuroimage. 2005;25(3):859–67.
    The problem of selecting a threshold for the statistical parameter maps in functional MRI (fMRI) is a delicate issue. The use of advanced test statistics and/or the complex dependence structure of fMRI noise may preclude parametric statistical methods for finding appropriate thresholds. Non-parametric statistical methodology has been presented as a feasible alternative. In this paper, we discuss resampling methods for finding thresholds in single subject fMRI analysis. It is shown that the presence of a BOLD response in the time series biases the estimation of the temporal autocorrelation, which in turn leads to biased thresholds. Therefore, proposed resampling methods based on Fourier and wavelet transforms, which employ implicit and weak models of the temporal noise characteristic, may produce erroneous thresholds. In contrast, resampling based on a pre-whitening transform, which is driven by an explicit noise model, is robust to the presence of a BOLD response. The size of the bias is, however, largely dependent on the complexity of the experimental design. While blocked designs can induce large biases, event-related designs generate significantly smaller biases. Results supporting these claims are provided.
  • Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin CF, Kikinis R, Shenton ME. Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study. Biol Psychiatry. 2005;58(6):468–78.
    BACKGROUND: Using diffusion tensor imaging (DTI), we previously reported abnormalities in two critical white matter tracts in schizophrenia, the uncinate fasciculus (UF) and the cingulum bundle (CB), both related to fronto-temporal connectivity. Here, we investigate these two bundles in unmedicated subjects with schizotypal personality disorder (SPD). METHODS: Fifteen male SPD subjects and 15 male control subjects were scanned with line-scan DTI. Fractional anisotropy (FA) and mean diffusivity (D(m)) were used to quantify water diffusion, and cross-sectional area was defined with a directional threshold method. Exploratory correlation analyses were evaluated with Spearman’s rho, followed by post hoc hierarchical regression analyses. RESULTS: We found bilaterally reduced FA in the UF of SPD subjects. For CB, there was no significant group difference for FA or D(m) measures. Additionally, in SPD, reduced FA in the right UF was correlated with clinical symptoms, including ideas of reference, suspiciousness, restricted affect, and social anxiety. In contrast, left UF area was correlated with measures of cognitive function, including general intelligence, verbal and visual memory, and executive performance. CONCLUSIONS: These findings in SPD suggest altered fronto-temporal connectivity through the UF, similar to findings in schizophrenia, and intact neocortical-limbic connectivity through the CB, in marked contrast with what has been reported in schizophrenia.
  • Limperopoulos C, Soul JS, Haidar H, Hüppi PS, Bassan H, Warfield SK, Robertson RL, Moore M, Akins P, Volpe JJ, Plessis A e J du. Impaired trophic interactions between the cerebellum and the cerebrum among preterm infants. Pediatrics. 2005;116(4):844–50.
    BACKGROUND: Advanced neuroimaging techniques have brought increasing recognition of cerebellar injury among premature infants. The developmental relationship between early brain injury and effects on the cerebrum and cerebellum remains unclear. OBJECTIVES: To examine whether cerebral parenchymal brain lesions among preterm infants are associated with subsequent decreases in cerebellar volume and, conversely, whether primary cerebellar injury is associated with decreased cerebral brain volumes, with advanced, 3-dimensional, volumetric MRI at term gestational age equivalent. METHODS: Total cerebellar volumes and cerebellar gray and myelinated white matter volumes were determined through manual outlining for 74 preterm infants with unilateral periventricular hemorrhagic infarction (14 infants), bilateral diffuse periventricular leukomalacia (20 infants), cerebellar hemorrhage (10 infants), or normal term gestational age equivalent MRI findings (30 infants). Total brain and right/left cerebral and cerebellar hemispheric volumes were calculated. RESULTS: Unilateral cerebral brain injury was associated with significantly decreased volume of the contralateral cerebellar hemisphere. Conversely, unilateral primary cerebellar injury was associated with a contralateral decrease in supratentorial brain volume. Cerebellar gray matter and myelinated white matter volumes were reduced significantly not only among preterm infants with primary cerebellar hemorrhage but also among infants with cerebral parenchymal brain injury. CONCLUSIONS: These data suggest strongly that both reduction in contralateral cerebellar volume with unilateral cerebral parenchymal injury and reduction in total cerebellar volume with bilateral cerebral lesions are related to trophic transsynaptic effects. Early-life cerebellar injury may contribute importantly to the high rates of cognitive, behavioral, and motor deficits reported for premature infants.
  • Tsai A, Wells WM III, Warfield SK, Willsky AS. An EM Algorithm for Shape Classification Based on Level Sets. Med Image Anal. 2005;9(5):491–502.
    In this paper, we propose an expectation-maximization (EM) approach to separate a shape database into different shape classes, while simultaneously estimating the shape contours that best exemplify each of the different shape classes. We begin our formulation by employing the level set function as the shape descriptor. Next, for each shape class we assume that there exists an unknown underlying level set function whose zero level set describes the contour that best represents the shapes within that shape class. The level set function for each example shape in the database is modeled as a noisy measurement of the appropriate shape class’s unknown underlying level set function. Based on this measurement model and the judicious introduction of the class labels as the hidden data, our EM formulation calculates the labels for shape classification and estimates the shape contours that best typify the different shape classes. This resulting iterative algorithm is computationally efficient, simple, and accurate. We demonstrate the utility and performance of this algorithm by applying it to two medical applications.