Jue Wu

An open source multivariate framework for n-tissue segmentation with evaluation on public data.

We introduce Atropos, an ITK-based multivariate n-class open source segmentation algorithm distributed with ANTs (http://www.picsl.upenn.edu/ANTs). The Bayesian formulation of the segmentation problem is solved using the Expectation Maximization (EM) algorithm with the modeling of the class intensities based on either parametric or non-parametric finite mixtures. Atropos is capable of incorporating spatial prior probability maps (sparse), prior label maps and/or Markov Random Field (MRF) modeling. Atropos has also been efficiently implemented to handle large quantities of possible labelings (in the experimental section, we use up to 69 classes) with a minimal memory footprint. This work describes the technical and implementation aspects of Atropos and evaluates its performance on two different ground-truth datasets. First, we use the BrainWeb dataset from Montreal Neurological Institute to evaluate three-tissue segmentation performance via (1) K-means segmentation without use of template data; (2) MRF segmentation with initialization by prior probability maps derived from a group template; (3) Prior-based segmentation with use of spatial prior probability maps derived from a group template. We also evaluate Atropos performance by using spatial priors to drive a 69-class EM segmentation problem derived from the Hammers atlas from University College London. These evaluation studies, combined with illustrative examples that exercise Atropos options, demonstrate both performance and wide applicability of this new platform-independent open source segmentation tool.

Associations between children's socioeconomic status and prefrontal cortical thickness

Childhood socioeconomic status (SES) predicts executive function performance and measures of prefrontal cortical function, but little is known about its anatomical correlates. Structural MRI and demographic data from a sample of 283 healthy children from the NIH MRI Study of Normal Brain Development were used to investigate the relationship between SES and prefrontal cortical thickness. Specifically, we assessed the association between two principal measures of childhood SES, family income and parental education, and gray matter thickness in specific subregions of prefrontal cortex and on the asymmetry of these areas. After correcting for multiple comparisons and controlling for potentially confounding variables, parental education significantly predicted cortical thickness in the right anterior cingulate gyrus and left superior frontal gyrus. These results suggest that brain structure in frontal regions may provide a meaningful link between SES and cognitive function among healthy, typically developing children.

A Segmentation Model Using Compound Markov Random Fields Based on a Boundary Model

Markov random field (MRF) theory has been widely applied to the challenging problem of image segmentation. In this paper, we propose a new nontexture segmentation model using compound MRFs, in which the original label MRF is coupled with a new boundary MRF to help improve the segmentation performance. The boundary model is relatively general and does not need prior training on boundary patterns. Unlike some existing related work, the proposed method offers a more compact interaction between label and boundary MRFs. Furthermore, our boundary model systematically takes into account all the possible scenarios of a single edge existing in a 3times3 neighborhood and, thus, incorporates sophisticated prior information about the relation between label and boundary. It is experimentally shown that the proposed model can segment objects with complex boundaries and at the same time is able to work under noise corruption. The new method has been applied to medical image segmentation. Experiments on synthetic images and real clinical datasets show that the proposed model is able to produce more accurate segmentation results and satisfactorily keep the delicate boundary. It is also less sensitive to noise in both high and low signal-to-noise ratio regions than some of the existing models in common use

Evaluation of automatic neonatal brain segmentation algorithms:the NeoBrainS12 challenge

A number of algorithms for brain segmentation in preterm born infants have been published, but a reliable comparison of their performance is lacking. The NeoBrainS12 study (http://neobrains12.isi.uu.nl), providing three different image sets of preterm born infants, was set up to provide such a comparison. These sets are (i) axial scans acquired at 40 weeks corrected age, (ii) coronal scans acquired at 30 weeks corrected age and (iii) coronal scans acquired at 40 weeks corrected age. Each of these three sets consists of three T1- and T2-weighted MR images of the brain acquired with a 3T MRI scanner. The task was to segment cortical grey matter, non-myelinated and myelinated white matter, brainstem, basal ganglia and thalami, cerebellum, and cerebrospinal fluid in the ventricles and in the extracerebral space separately. Any team could upload the results and all segmentations were evaluated in the same way. This paper presents the results of eight participating teams. The results demonstrate that the participating methods were able to segment all tissue classes well, except myelinated white matter.

Accuracy of the cylinder approximation for susceptometric measurement of intravascular oxygen saturation

Susceptometry‐based MR oximetry has previously been shown suitable for quantifying hemoglobin oxygen saturation in large vessels for studying vascular reactivity and quantification of global cerebral metabolic rate of oxygen utilization. A key assumption underlying this method is that large vessels can be modeled as long paramagnetic cylinders. However, bifurcations, tapering, noncircular cross‐section, and curvature of these vessels produce substantial deviations from cylindrical geometry, which may lead to errors in hemoglobin oxygen saturation quantification. Here, the accuracy of the “long cylinder” approximation is evaluated via numerical computation of the induced magnetic field from 3D segmented renditions of three veins of interest (superior sagittal sinus, femoral and jugular vein). At a typical venous oxygen saturation of 65%, the absolute error in hemoglobin oxygen saturation estimated via a closed‐form cylinder approximation was 2.6% hemoglobin oxygen saturation averaged over three locations in the three veins studied and did not exceed 5% for vessel tilt angles <30° at any one location. In conclusion, the simulation results provide a significant level of confidence for the validity of the cylinder approximation underlying MR susceptometry‐based oximetry of large vessels. Magn Reson Med, 2012.

Multiresolution Image Registration Based on Kullback-Leibler Distance

This paper extends our prior work on multi-modal image registration based on the a priori knowledge of the joint intensity dis- tribution that we expect to obtain, and Kullback-Leibler distance. This expected joint distribution can be estimated from pre-aligned training images. Experimental results show that, as compared with the Mutual Information and Approximate Maximum Likelihood based registration methods, the new method has longer capture range at different image resolutions, which can lead to a more robust image registration method. Moreover, with a simple interpolation algorithm based on non-grid point random sampling, the proposed method can avoid interpolation artifacts at the low resolution registration. Finally, it is experimentally demon- strated that our method is applicable to a variety of imaging modalities.

Multimodal Brain Image Registration Based on Wavelet Transform Using SAD and MI

The multiresolution approach is commonly used to speed up the mutual-information (MI) based registration process. Conventionally, a Gaussian pyramid is often used as a multiresolution representation. However, in multi-modal medical image registration, MI-based methods with Gaussian pyramid may suffer from the problem of short capture ranges especially at the lower resolution levels. This paper proposes a novel and straightforward multimodal image registration method based on wavelet representation, in which two matching criteria are used including sum of difference (SAD) for improving the registration robustness and MI for assuring the registration accuracy. Experimental results show that the proposed method obtains a longer capture range than the traditional MI-based Gaussian pyramid method meanwhile maintaining comparable accuracy.

A novel framework for segmentation of deep brain structures based on Markov dependence tree.

The aim of this work is to develop a new framework for multi-object segmentation of deep brain structures (caudate nucleus, putamen and thalamus) in medical brain images. Deep brain segmentation is difficult and challenging because the structures of interest are of relatively small size and have significant shape variations. The structure boundaries may be blurry or even missing, and the surrounding background is full of irrelevant edges. To tackle these problems, we propose a template-based framework to fuse the information of edge features, region statistics and inter-structure constraints for detecting and locating all target brain structures such that initialization by hand is unnecessary. The multi-object template is organized in the form of a hierarchical Markov dependence tree (MDT), and multiple objects are efficiently matched to a target image by a top-to-down optimization strategy. The final segmentation is obtained through refinement by a B-spline based non-rigid registration between the exemplar image and the target image. Our approach needs only one example as training data. We have validated the proposed method on a publicly available T1-weighted magnetic resonance image database with expert-segmented brain structures. In the experiments, the proposed approach has obtained encouraging results with 0.80 Dice score for the caudate nuclei, 0.81 Dice score for the putamina and 0.84 Dice score for the thalami on average.

Shape-Based Image Segmentation Using Normalized Cuts

To segment a whole object from an image is an essential and challenging task in image processing. In this paper, we propose a hybrid segmentation algorithm which combines prior shape information with normalized cut. With the help of shape information, we can utilize normalized cut to correctly segment the target whose boundary may be corrupted by noise or outliers. At the same time, we introduce the use of segmentation results of the normalized cut to guide the shape model, and thus avoid searching the shape space. The proposed method was demonstrated to be effective by our experiments on both synthetic and real data.

An open-source automated platform for three-dimensional visualization of subdural electrodes using CT-MRI coregistration

Visualizing implanted subdural electrodes in three‐dimensional (3D) space can greatly aid in planning, executing, and validating resection in epilepsy surgery. Coregistration software is available, but cost, complexity, insufficient accuracy, or validation limit adoption. We present a fully automated open‐source application, based on a novel method using postimplant computerized tomography (CT) and postimplant magnetic resonance (MR) images, for accurately visualizing intracranial electrodes in 3D space.