Publications by Year: 2012


This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down.

Shackleford JA, Shusharina N, Verberg J, Warmerdam G, Winey B, Neuner M, Steininger P, Arbisser A, Golland P. Plastimatch 1.6 - Current Capabilities and Future Directions. Int Conf Med Image Comput Comput Assist Interv. Workshop on Image-Guidance and Multimodal Dose Planning in Radiation Therapy. 2012;15(WS)

Open-source software provides an economic benefit by reducing duplicated development effort, and advances science knowledge by fostering a culture of reproducible experimentation. This paper describes recent advances in the Plastimatch open software suite, which implements a broad set of useful tools for research and practice in radiotherapy and medical imaging. The focus of this paper is to highlight recent advancements, including 2D-3D registration, GPU-accelerated mutual information, analytic regularization of B-spline registration, automatic 3D feature detection and feature matching, and radiotherapy plan evaluation tools.

Janoos F, Lee W, Subrahmanya N, Mórocz IA, Wells WM. Identification of Recurrent Patterns in the Activation of Brain Networks. Adv. In Neural Info. Proc. Sys (NIPS) 2012;:1-9.

Identifying patterns from the neuroimaging recordings of brain activity related to the unobservable psychological or mental state of an individual can be treated as a unsupervised pattern recognition problem. The main challenges, however, for such an analysis of fMRI data are: a) defining a physiologically meaningful feature-space for representing the spatial patterns across time; b) dealing with the high-dimensionality of the data; and c) robustness to the various artifacts and confounds in the fMRI time-series. In this paper, we present a network-aware feature-space to represent the states of a general network, that enables comparing and clustering such states in a manner that is a) meaningful in terms of the network connectivity structure; b)computationally efficient; c) low-dimensional; and d) relatively robust to structured and random noise artifacts. This feature-space is obtained from a spherical relaxation of the transportation distance metric which measures the cost of trans- porting “mass over the network to transform one function into another. Through theoretical and empirical assessments, we demonstrate the accuracy and efficiency of the approximation, especially for large problems.

Fedorov A, Tuncali K, Fennessy FM, Tokuda J, Hata N, Wells WM, Kikinis R, Tempany CM. Image Registration for Targeted MRI-guided Transperineal Prostate Biopsy. J Magn Reson Imaging 2012;36(4):987-92.
PURPOSE: To develop and evaluate image registration methodology for automated re-identification of tumor-suspicious foci from preprocedural MR exams during MR-guided transperineal prostate core biopsy. MATERIALS AND METHODS: A hierarchical approach for automated registration between planning and intra-procedural T2-weighted prostate MRI was developed and evaluated on the images acquired during 10 consecutive MR-guided biopsies. Registration accuracy was quantified at image-based landmarks and by evaluating spatial overlap for the manually segmented prostate and sub-structures. Registration reliability was evaluated by simulating initial mis-registration and analyzing the convergence behavior. Registration precision was characterized at the planned biopsy targets. RESULTS: The total computation time was compatible with a clinical setting, being at most 2 min. Deformable registration led to a significant improvement in spatial overlap of the prostate and peripheral zone contours compared with both rigid and affine registration. Average in-slice landmark registration error was 1.3 ± 0.5 mm. Experiments simulating initial mis-registration resulted in an estimated average capture range of 6 mm and an average in-slice registration precision of ±0.3 mm. CONCLUSION: Our registration approach requires minimum user interaction and is compatible with the time constraints of our interventional clinical workflow. The initial evaluation shows acceptable accuracy, reliability and consistency of the method.
Gholami B, Bailey JM, Haddad WM, Tannenbaum AR. Clinical Decision Support and Closed-Loop Control for Cardiopulmonary Management and Intensive Care Unit Sedation Using Expert Systems. IEEE Trans Control Syst Technol 2012;20(5):1343-1350.
Patients in the intensive care unit (ICU) who require mechanical ventilation due to acute respiratory failure also frequently require the administration of sedative agents. The need for sedation arises both from patient anxiety due to the loss of personal control and the unfamiliar and intrusive environment of the ICU, and also due to pain or other variants of noxious stimuli. While physicians select the agent(s) used for sedation and cardiovascular function, the actual administration of these agents is the responsibility of the nursing staff. If clinical decision support systems and closed-loop control systems could be developed for critical care monitoring and lifesaving interventions as well as the administration of sedation and cardiopulmonary management, the ICU nurse could be released from the intense monitoring of sedation, allowing her/him to focus on other critical tasks. One particularly attractive strategy is to utilize the knowledge and experience of skilled clinicians, capturing explicitly the rules expert clinicians use to decide on how to titrate drug doses depending on the level of sedation. In this paper, we extend the deterministic rule-based expert system for cardiopulmonary management and ICU sedation framework presented in [1] to a stochastic setting by using probability theory to quantify uncertainty and hence deal with more realistic clinical situations.
Donnell LJO, Wells WM, Golby AJ, Westin C-F. Unbiased groupwise registration of white matter tractography. Med Image Comput Comput Assist Interv 2012;15(Pt 3):123-30.
We present what we believe to be the first investigation into unbiased multi-subject registration of whole brain diffusion tractography of the white matter. To our knowledge, this is also the first entropy-based objective function applied to fiber tract registration. To define the probability of fiber trajectories for the computation of entropy, we take advantage of a pairwise fiber distance used as the basis for a Gaussian-like kernel. By employing several values of the kernel’s scale parameter, the method is inherently multi-scale. Results of experiments using synthetic and real datasets demonstrate the potential of the method for simultaneous joint registration of tractography.
Wachinger C, Golland P. Spectral label fusion. Med Image Comput Comput Assist Interv 2012;15(Pt 3):410-7.
We present a new segmentation approach that combines the strengths of label fusion and spectral clustering. The result is an atlas-based segmentation method guided by contour and texture cues in the test image. This offers advantages for datasets with high variability, making the segmentation less prone to registration errors. We achieve the integration by letting the weights of the graph Laplacian depend on image data, as well as atlas-based label priors. The extracted contours are converted to regions, arranged in a hierarchy depending on the strength of the separating boundary. Finally, we construct the segmentation by a region-wise, instead of voxel-wise, voting, increasing the robustness. Our experiments on cardiac MRI show a clear improvement over majority voting and intensity-weighted label fusion.
Risholm P, Janoos F, Pursley J, Fedorov A, Tempany CM, Cormack RA, Wells WM. Selection of Optimal Hyper-Parameters for Estimation of Uncertainty in MRI-TRUS Registration of the Prostate. Med Image Comput Comput Assist Interv 2012;15(Pt 3):107-14.
Transrectal ultrasound (TRUS) facilitates intra-treatment delineation of the prostate gland (PG) to guide insertion of brachytherapy seeds, but the prostate substructure and apex are not always visible which may make the seed placement sub-optimal. Based on an elastic model of the prostate created from MRI, where the prostate substructure and apex are clearly visible, we use a Bayesian approach to estimate the posterior distribution on deformations that aligns the pre-treatment MRI with intra-treatment TRUS. Without apex information in TRUS, the posterior prediction of the location of the prostate boundary, and the prostate apex boundary in particular, is mainly determined by the pseudo stiffness hyper-parameter of the prior distribution. We estimate the optimal value of the stiffness through likelihood maximization that is sensitive to the accuracy as well as the precision of the posterior prediction at the apex boundary. From a data-set of 10 pre- and intra-treatment prostate images with ground truth delineation of the total PG, 4 cases were used to establish an optimal stiffness hyper-parameter when 15% of the prostate delineation was removed to simulate lack of apex information in TRUS, while the remaining 6 cases were used to cross-validate the registration accuracy and uncertainty over the PG and in the apex.
Savadjiev P, Rathi Y, Bouix S, Verma R, Westin C-F. Multi-scale characterization of white matter tract geometry. Med Image Comput Comput Assist Interv 2012;15(Pt 3):34-41.
The geometry of white matter tracts is of increased interest for a variety of neuroscientific investigations, as it is a feature reflective of normal neurodevelopment and disease factors that may affect it. In this paper, we introduce a novel method for computing multi-scale fibre tract shape and geometry based on the differential geometry of curve sets. By measuring the variation of a curve’s tangent vector at a given point in all directions orthogonal to the curve, we obtain a 2D "dispersion distribution function" at that point. That is, we compute a function on the unit circle which describes fibre dispersion, or fanning, along each direction on the circle. Our formulation is then easily incorporated into a continuous scale-space framework. We illustrate our method on different fibre tracts and apply it to a population study on hemispheric lateralization in healthy controls. We conclude with directions for future work.
Gholami B, Norton I, Tannenbaum AR, Agar NYR. Recursive feature elimination for brain tumor classification using desorption electrospray ionization mass spectrometry imaging. Conf Proc IEEE Eng Med Biol Soc 2012;2012:5258-61.
The metabolism and composition of lipids is of increasing interest for understanding and detecting disease processes. Lipid signatures of tumor type and grade have been demonstrated using magnetic resonance spectroscopy. Clinical management and ultimate prognosis of brain tumors depend largely on the tumor type, subtype, and grade. Mass spectrometry, a well-known analytical technique used to identify molecules in a given sample based on their mass, can significantly improve the problem of tumor type classification. This work focuses on the problem of identifying lipid features to use as input for classification. Feature selection could result in improvements in classifier performance, discovery of biomarkers, improved data interpretation, and patient treatment.