Publications by Year: 2006

2006

Kindlmann G, Tricoche X, Westin CF. Anisotropy creases delineate white matter structure in diffusion tensor MRI. Med Image Comput Comput Assist Interv. 2006;9(Pt 1):126–33.
Current methods for extracting models of white matter architecture from diffusion tensor MRI are generally based on fiber tractography. For some purposes a compelling alternative may be found in analyzing the first and second derivatives of diffusion anisotropy. Anisotropy creases are ridges and valleys of locally extremal anisotropy, where the gradient of anisotropy is orthogonal to one or more eigenvectors of its Hessian. We propose that anisotropy creases provide a basis for extracting a skeleton of white matter pathways, in that ridges of anisotropy coincide with interiors of fiber tracts, and valleys of anisotropy coincide with the interfaces between adjacent but distinctly oriented tracts. We describe a crease extraction algorithm that generates high-quality polygonal models of crease surfaces, then demonstrate the method on a measured diffusion tensor dataset, and visualize the result in combination with tractography to confirm its anatomic relevance.
Bergmann O, Kindlmann G, Lundervold A, Westin CF. Diffusion k-tensor estimation from Q-ball imaging using discretized principal axes. Med Image Comput Comput Assist Interv. 2006;9(Pt 2):268–75.
A reoccurring theme in the diffusion tensor imaging literature is the per-voxel estimation of a symmetric 3 x 3 tensor describing the measured diffusion. In this work we attempt to generalize this approach by calculating 2 or 3 or up to k diffusion tensors for each voxel. We show that our procedure can more accurately describe the diffusion particularly when crossing fibers or fiber-bundles are present in the datasets.
Dauguet J, Peled S, Berezovskii V, Delzescaux T, Warfield SK, Born R, Westin CF. 3D histological reconstruction of fiber tracts and direct comparison with diffusion tensor MRI tractography. Med Image Comput Comput Assist Interv. 2006;9(Pt 1):109–16.
A classical neural tract tracer, WGA-HRP, was injected at multiple sites within the brain of a macaque monkey. Histological sections of the labeled fiber tracts were reconstructed in 3D, and the fibers were segmented and registered with the anatomical post-mortem MRI from the same animal. Fiber tracing along the same pathways was performed on the DTI data using a classical diffusion tracing technique. The fibers derived from the DTI were compared with those segmented from the histology in order to evaluate the performance of DTI fiber tracing. While there was generally good agreement between the two methods, our results reveal certain limitations of DTI tractography, particularly at regions of fiber tract crossing or bifurcation.
Estepar RSJ, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Accurate airway wall estimation using phase congruency. Med Image Comput Comput Assist Interv. 2006;9(Pt 2):125–34.
Quantitative analysis of computed tomographic (CT) images of the lungs is becoming increasingly useful in the medical and surgical management of subjects with Chronic Obstructive Pulmonary Disease (COPD). Current methods for the assessment of airway wall work well in idealized models of the airway. We propose a new method for airway wall detection based on phase congruency. This method does not rely on either a specific model of the airway or the point spread function of the scanner. Our results show that our method gives a better localization of the airway wall than "full width at a half max" and is less sensitive to different reconstruction kernels and radiation doses.
Goldberg-Zimring D, Warfield SK. Novel image processing techniques to better understand white matter disruption in multiple sclerosis. Autoimmun Rev. 2006;5(8):544–8.
In Multiple Sclerosis (MS) patients, conventional magnetic resonance imaging (MRI) shows a pattern of white matter (WM) disruption but may also overlook some WM damage. Diffusion tensor MRI (DT-MRI) can provide important in-vivo information about fiber direction that is not provided by conventional MRI. The geometry of diffusion tensors can quantitatively characterize the local structure in tissues. The integration of both conventional MRI and DT-MRI measures together with connectivity-based regional assessment provide a better understanding of the nature and the location of WM abnormalities. Image processing and visualization techniques have been developed and applied to study conventional MRI and DT-MRI of MS patients. These include methods of: Image Segmentation for identifying the different areas of the brain as well as to discriminate normal from abnormal WM, Computerized Atlases, which include structural information obtained from a set of subjects, and Tractographies which can aid in the delineation of WM fiber tracts by tracking connected diffusion tensors. These new techniques hold out the promise of improving our understanding of WM architecture and its disruption in diseases such as MS. In the present study, we review the work that has been done in the development of these techniques and illustrate their applications.
Hershkovitz E, Sapiro G, Tannenbaum A, Williams LD. Statistical analysis of RNA backbone. IEEE/ACM Trans Comput Biol Bioinform. 2006;3(1):33–46.
Local conformation is an important determinant of RNA catalysis and binding. The analysis of RNA conformation is particularly difficult due to the large number of degrees of freedom (torsion angles) per residue. Proteins, by comparison, have many fewer degrees of freedom per residue. In this work, we use and extend classical tools from statistics and signal processing to search for clusters in RNA conformational space. Results are reported both for scalar analysis, where each torsion angle is separately studied, and for vectorial analysis, where several angles are simultaneously clustered. Adapting techniques from vector quantization and clustering to the RNA structure, we find torsion angle clusters and RNA conformational motifs. We validate the technique using well-known conformational motifs, showing that the simultaneous study of the total torsion angle space leads to results consistent with known motifs reported in the literature and also to the finding of new ones.
Kuroki N, Shenton ME, Salisbury DF, Hirayasu Y, Onitsuka T, Ersner-Hershfield H, Yurgelun-Todd D, Kikinis R, Jolesz FA, McCarley RW. Middle and inferior temporal gyrus gray matter volume abnormalities in first-episode schizophrenia: an MRI study. Am J Psychiatry. 2006;163(12):2103–10.
OBJECTIVE: Magnetic resonance imaging (MRI) studies of schizophrenia reveal temporal lobe structural brain abnormalities in the superior temporal gyrus and the amygdala-hippocampal complex. However, the middle and inferior temporal gyri have received little investigation, especially in first-episode schizophrenia. METHOD: High-spatial-resolution MRI was used to measure gray matter volume in the inferior, middle, and superior temporal gyri in 20 patients with first-episode schizophrenia, 20 patients with first-episode affective psychosis, and 23 healthy comparison subjects. RESULTS: Gray matter volume in the middle temporal gyrus was smaller bilaterally in patients with first-episode schizophrenia than in comparison subjects and in patients with first-episode affective psychosis. Posterior gray matter volume in the inferior temporal gyrus was smaller bilaterally in both patient groups than in comparison subjects. Among the superior, middle, and inferior temporal gyri, the left posterior superior temporal gyrus gray matter in the schizophrenia group had the smallest volume, the greatest percentage difference, and the largest effect size in comparisons with healthy comparison subjects and with affective psychosis patients. CONCLUSIONS: Smaller gray matter volumes in the left and right middle temporal gyri and left posterior superior temporal gyrus were present in schizophrenia but not in affective psychosis at first hospitalization. In contrast, smaller bilateral posterior inferior temporal gyrus gray matter volume is present in both schizophrenia and affective psychosis at first hospitalization. These findings suggest that smaller gray matter volumes in the dorsal temporal lobe (superior and middle temporal gyri) may be specific to schizophrenia, whereas smaller posterior inferior temporal gyrus gray matter volumes may be related to pathology common to both schizophrenia and affective psychosis.
Mewes AUJ, Hüppi PS, Als H, Rybicki FJ, Inder TE, McAnulty GB, Mulkern RV, Robertson RL, Rivkin MJ, Warfield SK. Regional brain development in serial magnetic resonance imaging of low-risk preterm infants. Pediatrics. 2006;118(1):23–33.
OBJECTIVE: MRI studies have shown that preterm infants with brain injury have altered brain tissue volumes. Investigation of preterm infants without brain injury offers the opportunity to define the influence of early birth on brain development and provide normative data to assess effects of adverse conditions on the preterm brain. In this study, we investigated serial MRI of low-risk preterm infants with the aim to identify regions of altered brain development. METHODS: Twenty-three preterm infants appropriate for gestational age without magnetic resonance-visible brain injury underwent MRI twice at 32 and at 42 weeks’ postmenstrual age. Fifteen term infants were scanned 2 weeks after birth. Brain tissue classification and parcellation were conducted to allow comparison of regional brain tissue volumes. Longitudinal brain growth was assessed from preterm infants’ serial scans. RESULTS: At 42 weeks’ postmenstrual age, gray matter volumes were not different between preterm and term infants. Myelinated white matter was decreased, as were unmyelinated white matter volumes in the region including the central gyri. The gray matter proportion of the brain parenchyma constituted 30% and 37% at 32 and 42 weeks’ postmenstrual age, respectively. CONCLUSIONS: This MRI study of preterm infants appropriate for gestational age and without brain injury establishes the influence of early birth on brain development. No decreased cortical gray matter volumes were found, which is in contrast to findings in preterm infants with brain injury. Moderately decreased white matter volumes suggest an adverse influence of early birth on white matter development. We identified a sharp increase in cortical gray matter volume in preterm infants’ serial data, which may correspond to a critical period for cortical development.
Niethammer M, Kalies WD, Mischaikow K, Tannenbaum A. On the detection of simple points in higher dimensions using cubical homology. IEEE Trans Image Process. 2006;15(8):2462–9.
Simple point detection is an important task for several problems in discrete geometry, such as topology preserving thinning in image processing to compute discrete skeletons. In this paper, the approach to simple point detection is based on techniques from cubical homology, a framework ideally suited for problems in image processing. A (d-dimensional) unitary cube (for a d-dimensional digital image) is associated with every discrete picture element, instead of a point in epsilon(d) (the d-dimensional Euclidean space) as has been done previously. A simple point in this setting then refers to the removal of a unitary cube without changing the topology of the cubical complex induced by the digital image. The main result is a characterization of a simple point p (i.e., simple unitary cube) in terms of the homology groups of the (3d - 1) neighborhood of p for arbitrary, finite dimensions