Publications by Year: 2009


Malcolm JG, Shenton ME, Rathi Y. Neural Tractography using an Unscented Kalman Filter. Inf Process Med Imaging. 2009;21:126–38.
We describe a technique to simultaneously estimate a local neural fiber model and trace out its path. Existing techniques estimate the local fiber orientation at each voxel independently so there is no running knowledge of confidence in the estimated fiber model. We formulate fiber tracking as recursive estimation: at each step of tracing the fiber, the current estimate is guided by the previous. To do this we model the signal as a mixture of Gaussian tensors and perform tractography within a filter framework. Starting from a seed point, each fiber is traced to its termination using an unscented Kalman filter to simultaneously fit the local model and propagate in the most consistent direction. Despite the presence of noise and uncertainty, this provides a causal estimate of the local structure at each point along the fiber. Synthetic experiments demonstrate that this approach reduces signal reconstruction error and significantly improves the angular resolution at crossings and branchings. In vivo experiments confirm the ability to trace out fibers in areas known to contain such crossing and branching while providing inherent path regularization.
Donnell LJO, Westin CF, Golby AJ. Tract-Based Morphometry for White Matter Group Analysis.​​​​​​​. Neuroimage. 2009;45(3):832–44.
We introduce an automatic method that we call tract-based morphometry, or TBM, for measurement and analysis of diffusion MRI data along white matter fiber tracts. Using subject-specific tractography bundle segmentations, we generate an arc length parameterization of the bundle with point correspondences across all fibers and all subjects, allowing tract-based measurement and analysis. In this paper we present a quantitative comparison of fiber coordinate systems from the literature and we introduce an improved optimal match method that reduces spatial distortion and improves intra- and inter-subject variability of FA measurements. We propose a method for generating arc length correspondences across hemispheres, enabling a TBM study of interhemispheric diffusion asymmetries in the arcuate fasciculus (AF) and cingulum bundle (CB). The results of this study demonstrate that TBM can detect differences that may not be found by measuring means of scalar invariants in entire tracts, such as the mean diffusivity (MD) differences found in AF. We report TBM results of higher fractional anisotropy (FA) in the left hemisphere in AF (caused primarily by lower lambda(3), the smallest eigenvalue of the diffusion tensor, in the left AF), and higher left hemisphere FA in CB (related to higher lambda(1), the largest eigenvalue of the diffusion tensor, in the left CB). By mapping the significance levels onto the tractography trajectories for each structure, we demonstrate the anatomical locations of the interhemispheric differences. The TBM approach brings analysis of DTI data into the clinically and neuroanatomically relevant framework of the tract anatomy.
Tristan-Vega A, Aja-Fernández S, Westin CF. On the blurring of the Funk–Radon transform in Q–ball imaging. Med Image Comput Comput Assist Interv. 2009;12(Pt 2):415–22.
One known issue in Q-Ball imaging is the blurring in the radial integral defining the Orientation Distribution Function of fiber bundles, due to the computation of the Funk-Radon Transform (FRT). Three novel techniques to overcome this problem are presented, all of them based upon different assumptions about the behavior of the attenuation signal outside the sphere densely sampled from HARDI data sets. A systematic study with synthetic data has been carried out to show that the FRT blurring is not as important as the error introduced by some unrealistic assumptions, and only one of the three techniques (the one with the less restrictive assumption) improves the accuracy of Q-Balls.
Sabuncu MR, Yeo BTT, Van Leemput K, Fischl B, Golland P. Nonparametric Mixture Models for Supervised Image Parcellation. Med Image Comput Comput Assist Interv. 2009;12(WS):301–313.
We present a nonparametric, probabilistic mixture model for the supervised parcellation of images. The proposed model yields segmentation algorithms conceptually similar to the recently developed label fusion methods, which register a new image with each training image separately. Segmentation is achieved via the fusion of transferred manual labels. We show that in our framework various settings of a model parameter yield algorithms that use image intensity information differently in determining the weight of a training subject during fusion. One particular setting computes a single, global weight per training subject, whereas another setting uses locally varying weights when fusing the training data. The proposed nonparametric parcellation approach capitalizes on recently developed fast and robust pairwise image alignment tools. The use of multiple registrations allows the algorithm to be robust to occasional registration failures. We report experiments on 39 volumetric brain MRI scans with expert manual labels for the white matter, cerebral cortex, ventricles and subcortical structures. The results demonstrate that the proposed nonparametric segmentation framework yields significantly better segmentation than state-of-the-art algorithms.
Kubicki M, Niznikiewicz M, Connor E, Ungar L, Nestor P, Bouix S, Dreusicke M, Kikinis R, McCarley R, Shenton M. Relationship Between White Matter Integrity, Attention, and Memory in Schizophrenia: A Diffusion Tensor Imaging Study. Brain Imaging Behav. 2009;3(2):191–201.
Attention and memory deficits are among the most prominent cognitive disturbances observed in schizophrenia. It has been suggested that a disruption in anatomical connectivity between areas involved in attentional control might be responsible for these abnormalities. We used Diffusion Tensor Tractography and Color Stroop/Negative Priming(NP) paradigm to investigate integrity of Cingulum Bundle(CB), the main white matter tract interconnecting these regions, and its relationship with executive functions in patients with schizophrenia and matched controls. The Fractional Anisotropy(FA), was calculated along the CB pathways, and correlated with reaction times for each Stroop item, and both Stroop, and NP effects. Patients with schizophrenia demonstrated decreased CB integrity and diminished NP effect, compared with controls, but both groups showed Stroop effect. For patients only, reaction times for every item, as well as for Stroop effect, correlated with left CB FA. These findings suggest that CB integrity disruptions might compromise the executive processes in schizophrenia.
Estepar RSJ, Westin CF, Vosburgh KG. Towards real time 2D to 3D registration for ultrasound-guided endoscopic and laparoscopic procedures. Int J Comput Assist Radiol Surg. 2009;4(6):549–60.
PURPOSE: A method to register endoscopic and laparoscopic ultrasound (US) images in real time with pre-operative computed tomography (CT) data sets has been developed with the goal of improving diagnosis, biopsy guidance, and surgical interventions in the abdomen. METHODS: The technique, which has the potential to operate in real time, is based on a new phase correlation technique: LEPART, which specifies the location of a plane in the CT data which best corresponds to the US image. Validation of the method was carried out using an US phantom with cyst regions and with retrospective analysis of data sets from animal model experiments. RESULTS: The phantom validation study shows that local translation displacements can be recovered for each US frame with a root mean squared error of 1.56 +/- 0.78 mm in less than 5 sec, using non-optimized algorithm implementations. CONCLUSION: A new method for multimodality (preoperative CT and intraoperative US endoscopic images) registration to guide endoscopic interventions was developed and found to be efficient using clinically realistic datasets. The algorithm is inherently capable of being implemented in a parallel computing system so that full real time operation appears likely.
Kindlmann GL, Estepar RSJ, Smith SM, Westin CF. Sampling and visualizing creases with scale-space particles. IEEE Trans Vis Comput Graph. 2009;15(6):1415–24.
Particle systems have gained importance as a methodology for sampling implicit surfaces and segmented objects to improve mesh generation and shape analysis. We propose that particle systems have a significantly more general role in sampling structure from unsegmented data. We describe a particle system that computes samplings of crease features (i.e. ridges and valleys, as lines or surfaces) that effectively represent many anatomical structures in scanned medical data. Because structure naturally exists at a range of sizes relative to the image resolution, computer vision has developed the theory of scale-space, which considers an n-D image as an (n+1)-D stack of images at different blurring levels. Our scale-space particles move through continuous four-dimensional scale-space according to spatial constraints imposed by the crease features, a particle-image energy that draws particles towards scales of maximal feature strength, and an inter-particle energy that controls sampling density in space and scale. To make scale-space practical for large three-dimensional data, we present a spline-based interpolation across scale from a small number of pre-computed blurrings at optimally selected scales. The configuration of the particle system is visualized with tensor glyphs that display information about the local Hessian of the image, and the scale of the particle. We use scale-space particles to sample the complex three-dimensional branching structure of airways in lung CT, and the major white matter structures in brain DTI.
Oguro S, Tokuda J, Elhawary H, Haker S, Kikinis R, Tempany CM, Hata N. MRI Signal Intensity Based B-Spline Nonrigid Registration for Pre- and Intraoperative Imaging during Prostate Brachytherapy. J Magn Reson Imaging. 2009;30(5):1052–8.
PURPOSE: To apply an intensity-based nonrigid registration algorithm to MRI-guided prostate brachytherapy clinical data and to assess its accuracy. MATERIALS AND METHODS: A nonrigid registration of preoperative MRI to intraoperative MRI images was carried out in 16 cases using a Basis-Spline algorithm in a retrospective manner. The registration was assessed qualitatively by experts’ visual inspection and quantitatively by measuring the Dice similarity coefficient (DSC) for total gland (TG), central gland (CG), and peripheral zone (PZ), the mutual information (MI) metric, and the fiducial registration error (FRE) between corresponding anatomical landmarks for both the nonrigid and a rigid registration method. RESULTS: All 16 cases were successfully registered in less than 5 min. After the nonrigid registration, DSC values for TG, CG, PZ were 0.91, 0.89, 0.79, respectively, the MI metric was -0.19 +/- 0.07 and FRE presented a value of 2.3 +/- 1.8 mm. All the metrics were significantly better than in the case of rigid registration, as determined by one-sided t-tests. CONCLUSION: The intensity-based nonrigid registration method using clinical data was demonstrated to be feasible and showed statistically improved metrics when compare to only rigid registration. The method is a valuable tool to integrate pre- and intraoperative images for brachytherapy.
Ou W, Nummenmaa A, Golland P, Hämäläinen MS. Multimodal functional imaging using fMRI-informed regional EEG/MEG source estimation. Conf Proc IEEE Eng Med Biol Soc. 2009;2009:1926–9.
We propose a novel method, fMRI-Informed Regional Estimation (FIRE), which utilizes information from fMRI in E/MEG source reconstruction. FIRE takes advantage of the spatial alignment between the neural and the vascular activities, while allowing for substantial differences in their dynamics. Furthermore, with the regional approach, FIRE can be efficiently applied to a dense grid of sources. Inspection of our optimization procedure reveals that FIRE is related to the re-weighted minimum-norm algorithms, the difference being that the weights in the proposed approach are computed from both the current estimates and fMRI data. Analysis of both simulated and human fMRI-MEG data shows that FIRE reduces the ambiguities in source localization present in the minimum-norm estimates. Comparisons with several joint fMRI-E/MEG algorithms demonstrate robustness of FIRE in the presence of sources silent to either fMRI or E/MEG measurements.