Publications

2004
Dickhaus CF, Burghart C, Tempany C, D'Amico A, Haker S, Kikinis R, Woern H. Workflow modeling and analysis of computer guided prostate brachytherapy under MR imaging control. Stud Health Technol Inform. 2004;98 :72-4.Abstract
We demonstrate that classical Business Process Reengineering (BPR) methods can be successfully applied to Computer Aided Surgery while increasing safety and efficiency of the overall procedure through an integrated Workflow Management System. Computer guided Prostate Brachytherapy, as a sophisticated treatment by an interdisciplinary team, is perfectly suited to apply our method. Detailed suggestions for improvement of the whole procedure could be derived by our modified BPR method.
Topgaard D, Martin RW, Sakellariou D, Meriles CA, Pines A. "Shim pulses" for NMR spectroscopy and imaging. Proc Natl Acad Sci U S A. 2004;101 (51) :17576-81.Abstract
A way to use adiabatic radiofrequency pulses and modulated magnetic-field gradient pulses, together constituting a "shim pulse," for NMR spectroscopy and imaging is demonstrated. These pulses capitalize on phase shifts derived from probe gradient coils to compensate for nonlinear intrinsic main magnetic field homogeneity for spectroscopy, as well as for deviations from linear gradients for imaging. This approach opens up the possibility of exploiting cheaper, less-than-perfect magnets and gradient coils for NMR applications.
Pettersson E, Topgaard D, Stilbs P, Söderman O. Surfactant/Nonionic polymer interaction. A NMR diffusometry and NMR electrophoretic investigation. Langmuir. 2004;20 (4) :1138-43.Abstract
The interaction between the nonionic polymer poly(ethylene oxide) (PEO) of molecular weight 20,000 and surfactants of various types [sodium dodecyl sulfate (SDS), dodecyl trimethylammonium bromide, octyl beta-D-glucoside, and potassium laurate] has been investigated in an aqueous solution at 25 degrees C by 1H NMR pulsed-gradient spin-echo self-diffusion techniques. The SDS/PEO study was further complemented by component-resolved 1H NMR-based studies of the electrophoretic mobility of PEO and the alkyl part of SDS under the same measurement conditions. Through such combined studies, a much more complete picture of the binding and aggregation processes becomes accessible.
Liger-Belair G, Topgaard D, Voisin C, Jeandet P. Is the wall of a cellulose fiber saturated with liquid whether or not permeable with CO2 dissolved molecules? Application to bubble nucleation in champagne wines. Langmuir. 2004;20 (10) :4132-8.Abstract
In this paper, the transversal diffusion coefficient D perpendicular of CO2 dissolved molecules through the wall of a hydrated cellulose fiber was approached, from the liquid bulk diffusion coefficient of CO2 dissolved molecules modified by an obstruction factor. The porous network between the cellulose microfibrils of the fiber wall was assumed being saturated with liquid. We retrieved information from previous NMR experiments on the self-diffusion of water in cellulose fibers to reach an order of magnitude for the transversal diffusion coefficient of CO2 molecules through the fiber wall. A value of about D perpendicular approximately 0.2D0 was proposed, D0 being the diffusion coefficient of CO2 molecules in the liquid bulk. Because most of bubble nucleation sites in a glass poured with carbonated beverage are cellulose fibers cast off from paper or cloth which floated from the surrounding air, or remaining from the wiping process, this result directly applies to the kinetics of carbon dioxide bubble formation from champagne and sparkling wines. If the cellulose fiber wall was impermeable with regard to CO2 dissolved molecules, it was suggested that the kinetics of bubbling would be about three times less than it is.
Maier SE, Vajapeyam S, Mamata H, Westin C-F, Jolesz FA, Mulkern RV. Biexponential diffusion tensor analysis of human brain diffusion data. Magn Reson Med. 2004;51 (2) :321-30.Abstract
Several studies have shown that in tissues over an extended range of b-factors, the signal decay deviates significantly from the basic monoexponential model. The true nature of this departure has to date not been identified. For the current study, line scan diffusion images of brain suitable for biexponential diffusion tensor analysis were acquired in normal subjects on a clinical MR system. For each of six noncollinear directions, 32 images with b-factors ranging from 5 to 5000 s/mm2 were collected. Biexponential fits yielded parameter maps for a fast and a slow diffusion component. A subset of the diffusion data, consisting of the images obtained at the conventional range of b-factors between 5 and 972 s/mm2, was used for monoexponential diffusion tensor analysis. Fractional anisotropy (FA) of the fast-diffusion component and the monoexponential fit exhibited no significant difference. FA of the slow-diffusion biexponential component was significantly higher, particularly in areas of lower fiber density. The principal diffusion directions for the two biexponential components and the monoexponential solution were largely the same and in agreement with known fiber tracts. The second and third diffusion eigenvector directions also appeared to be aligned, but they exhibited significant deviations in localized areas.
Brun A, Knutsson H, Park H-J, Shenton ME, Westin C-F. Clustering Fiber Traces Using Normalized Cuts. Med Image Comput Comput Assist Interv. 2004;3216/2004 (3216) :368-375.Abstract
In this paper we present a framework for unsupervised segmentation of white matter fiber traces obtained from diffusion weighted MRI data. Fiber traces are compared pairwise to create a weighted undirected graph which is partitioned into coherent sets using the normalized cut (N cut) criterion. A simple and yet effective method for pairwise comparison of fiber traces is presented which in combination with the N cut criterion is shown to produce plausible segmentations of both synthetic and real fiber trace data. Segmentations are visualized as colored stream-tubes or transformed to a segmentation of voxel space, revealing structures in a way that looks promising for future explorative studies of diffusion weighted MRI data.
Park H-J, Kubicki M, Westin C-F, Talos I-F, Brun A, Peiper S, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Method for combining information from white matter fiber tracking and gray matter parcellation. AJNR Am J Neuroradiol. 2004;25 (8) :1318-24.Abstract
We introduce a method for combining fiber tracking from diffusion-tensor (DT) imaging with cortical gray matter parcellation from structural high-spatial-resolution 3D spoiled gradient-recalled acquisition in the steady state images. We applied this method to a tumor case to determine the impact of the tumor on white matter architecture. We conclude that this new method for combining structural and DT imaging data is useful for understanding cortical connectivity and the localization of fiber tracts and their relationship with cortical anatomy and brain abnormalities.
Kozinska D, Holland CM, Krissian K, Westin C-F, Guttmann CRG. A method for the analysis of the geometrical relationship between white matter pathology and the vascular architecture of the brain. Neuroimage. 2004;22 (4) :1671-8.Abstract
A novel method for the visual and quantitative analysis of the geometrical relationship between the vascular architecture of the brain and white matter pathology is presented. The cerebro vascular system is implicated in the pathogenesis of many diseases of the cerebral white matter, for example, stroke, microcerebrovascular disease, and multiple sclerosis (MS). In our work, white matter lesions and vessels are depicted using magnetic resonance imaging (MRI) and extracted using image analysis techniques. We focus on measuring distance relationships between white matter lesions and vessels, and distribution of lesions with respect to vessel caliber. Vascular distance maps are generated by computing for each voxel the Euclidean distance to the closest vessel. Analogously, radius maps assign the radius of the closest vessel to each voxel in the image volume. The distance and radius maps are used to analyze the distribution of lesions with respect to the vessels' locations and their calibers. The method was applied to three MS patients to demonstrate its functionality and feasibility. Preliminary findings indicate that larger MS lesions tend to be farther from detected vessels and that the caliber of the vessels nearest to larger lesions tends to be smaller, suggesting a possible role of relative hypoperfusion or hypoxia in lesion formation.
Levitt JJ, Westin CF, Nestor PG, Estepar RSJ, Dickey CC, Voglmaier MM, Seidman LJ, Kikinis R, Jolesz FA, McCarley RW, et al. Shape of caudate nucleus and its cognitive correlates in neuroleptic-naive schizotypal personality disorder. Biol Psychiatry. 2004;55 (2) :177-84.Abstract
BACKGROUND: We measured the shape of the head of the caudate nucleus with a new approach based on magnetic resonance imaging (MRI) in schizotypal personality disorder (SPD) subjects in whom we previously reported decreased caudate nucleus volume. We believe MRI shape analysis complements traditional MRI volume measurements. METHODS: Magnetic resonance imaging scans were used to measure the shape of the caudate nucleus in 15 right-handed male subjects with SPD, who had no prior neuroleptic exposure, and in 14 matched normal comparison subjects. With MRI processing tools, we measured the head of the caudate nucleus using a shape index, which measured how much a given shape deviates from a sphere. RESULTS: In relation to comparison subjects, neuroleptic never-medicated SPD subjects had significantly higher (more "edgy") head of the caudate shape index scores, lateralized to the right side. Additionally, for SPD subjects, higher right and left head of the caudate SI scores correlated significantly with poorer neuropsychological performance on tasks of visuospatial memory and auditory/verbal working memory, respectively. CONCLUSIONS: These data confirm the value of measuring shape, as well as volume, of brain regions of interest and support the association of intrinsic pathology in the caudate nucleus, unrelated to neuroleptic medication, with cognitive abnormalities in the schizophrenia spectrum.
Park H-J, Westin C-F, Kubicki M, Maier SE, Niznikiewicz M, Baer A, Frumin M, Kikinis R, Jolesz FA, McCarley RW, et al. White matter hemisphere asymmetries in healthy subjects and in schizophrenia: a diffusion tensor MRI study. Neuroimage. 2004;23 (1) :213-23.Abstract
Hemisphere asymmetry was explored in normal healthy subjects and in patients with schizophrenia using a novel voxel-based tensor analysis applied to fractional anisotropy (FA) of the diffusion tensor. Our voxel-based approach, which requires precise spatial normalization to remove the misalignment of fiber tracts, includes generating a symmetrical group average template of the diffusion tensor by applying nonlinear elastic warping of the demons algorithm. We then normalized all 32 diffusion tensor MRIs from healthy subjects and 23 from schizophrenic subjects to the symmetrical average template. For each brain, six channels of tensor component images and one T2-weighted image were used for registration to match tensor orientation and shape between images. A statistical evaluation of white matter asymmetry was then conducted on the normalized FA images and their flipped images. In controls, we found left-higher-than-right anisotropic asymmetry in the anterior part of the corpus callosum, cingulum bundle, the optic radiation, and the superior cerebellar peduncle, and right-higher-than-left anisotropic asymmetry in the anterior limb of the internal capsule and the anterior limb's prefrontal regions, in the uncinate fasciculus, and in the superior longitudinal fasciculus. In patients, the asymmetry was lower, although still present, in the cingulum bundle and the anterior corpus callosum, and not found in the anterior limb of the internal capsule, the uncinate fasciculus, and the superior cerebellar peduncle compared to healthy subjects. These findings of anisotropic asymmetry pattern differences between healthy controls and patients with schizophrenia are likely related to neurodevelopmental abnormalities in schizophrenia.
Pujol S, Pecher M, Magne J-L, Cinquin P. A virtual reality based navigation system for endovascular surgery. Stud Health Technol Inform. 2004;98 :310-2.Abstract
Endovascular surgery provides a minimally invasive solution for the treatment of aortic aneurysms. Fluoroscopic guidance involves X-rays exposure and loss of space information. We have developed a navigation system allowing real-time visualisation of the endovascular tools in a 3D model of the vessels without any radiation exposure. A modified endoprosthesis is equipped with a magnetic sensor tracked by the Aurora magnetic localizer. The registration step uses 2.5D ultrasonography to replace pre-operative CT data in the Operating Room referential. The Virtual Reality based navigation system shows the location of the endoprosthesis inside a 3D CT model of the aorta. Endovascular procedure benefits from a reduced radiation exposure.
Boiman O, Peled S, Yeshurun Y. Detection of pseudoperiodic patterns using partial acquisition of magnetic resonance images. Magn Reson Imaging. 2004;22 (9) :1265-78.Abstract
Improving the resolution of magnetic resonance imaging (MRI), or, alternatively, reducing the acquisition time, can be quite beneficial for many applications. The main motivation of this work is the assumption that any information that is a priori available on the target image could be used to achieve this goal. In order to demonstrate this approach, we present a novel partial acquisition strategy and reconstruction algorithm, suitable for the special case of detection of pseudoperiodic patterns. Pseudoperiodic patterns are frequently encountered in the cerebral cortex due to its columnar functional organization (best exemplified by orientation columns and ocular dominance columns of the visual cortex). We present a new MRI research methodology, in which we seek an activity pattern, and a pattern-specific experiment is devised to detect it. Such specialized experiments extend the limits of conventional MRI experiments by substantially reducing the scan time. Using the fact that pseudoperiodic patterns are localized in the Fourier domain, we present an optimality criterion for partial acquisition of the MR signal and a strategy for obtaining the optimal discrete Fourier transform (DFT) coefficients. A by-product of this strategy is an optimal linear extrapolation estimate. We also present a nonlinear spectral extrapolation algorithm, based on projections onto convex sets (POCSs), used to perform the actual reconstruction. The proposed strategy was tested and analyzed on simulated signals and in MRI phantom experiments.
Mitsouras D, Hoge SW, Rybicki FJ, Kyriakos WE, Edelman A, Zientara GP. Non-Fourier-encoded parallel MRI using multiple receiver coils. Magn Reson Med. 2004;52 (2) :321-8.Abstract
This paper describes a general theoretical framework that combines non-Fourier (NF) spatially-encoded MRI with multichannel acquisition parallel MRI. The two spatial-encoding mechanisms are physically and analytically separable, which allows NF encoding to be expressed as complementary to the inherent encoding imposed by RF receiver coil sensitivities. Consequently, the number of NF spatial-encoding steps necessary to fully encode an FOV is reduced. Furthermore, by casting the FOV reduction of parallel imaging techniques as a dimensionality reduction of the k-space that is NF-encoded, one can obtain a speed-up of each digital NF spatial excitation in addition to accelerated imaging. Images acquired at speed-up factors of 2x to 8x with a four-element RF receiver coil array demonstrate the utility of this framework and the efficiency afforded by it.
Haidar H, Bouix S, Levitt J, McCarley RW, Shenton ME, Soul JS. An elliptic PDE approach for shape characterization. Conf Proc IEEE Eng Med Biol Soc. 2004;2 :1521-4.Abstract
This work presents a novel approach to analyze the shape of anatomical structures. Our methodology is rooted in classical physics and in particular Poisson's equation, a fundamental partial differential equation, The solution to this equation and more specifically its equipotential surfaces display properties that are useful for shape analysis. We present a numerical algorithm to calculate the length of streamlines formed by the gradient field of the solution to this equation for 2D and 3D objects. The length of the streamlines along the equipotential surfaces was used to build a new function which can characterize the shape of objects. We illustrate our method on 2D synthetic and natural shapes as well as 3D medical data.
2003
O'Donnell LJ, Sheerin BR, Hendry JM, Thatcher MJ, Thatcher WW, LeBlanc MM. 24-hour secretion patterns of plasma oestradiol 17beta in pony mares in late gestation. Reprod Domest Anim. 2003;38 (3) :233-5.Abstract
The mare exhibits nocturnal uterine contractions in the last 6 days of gestation. It is hypothesized that estradiol 17beta (O17beta) may be associated with the nightly increase in uterine contractions. The 24-h secretion pattern of plasma O17beta was measured in 3 pony mares in late gestation to identify changes in release as the mare neared parturition. Blood was collected weekly at 08:00 hours beginning on day 240 and every third day from day 330 until delivery. Serial blood samples were collected from each mare every 30-min for 24-h beginning on gestation day 310 and every sixth day thereafter until parturition. Concentrations of O17beta were elevated at night with lowest concentrations occurring directly before sunset (p < 0.01). The natural log of the variance was increased at sunset (p < 0.01) and was decreased during the 6-h period immediately after sunrise. This pattern was especially evident in the 6 days that preceded parturition. The contrast between nocturnal and daytime concentrations of O17beta in the last 6 days of gestation may contribute to night-time delivery in the mare.
Bujacz GD, Pasternak O, Fujimoto Y, Hashimoto Y, Sikorski MM, Jaskolski M. Crystallization and preliminary crystallographic studies of mung bean cytokinin-specific binding protein. Acta Crystallogr D Biol Crystallogr. 2003;59 (Pt 3) :522-5.Abstract
Cytokinins, or plant growth hormones, bind with very high affinity to cytokinin-specific binding proteins (CSBPs). Recombinant mung bean CSBP has been overexpressed in Escherichia coli and crystallized in complex with zeatin, a natural plant growth hormone. The crystals belong to the hexagonal system, space group P6(2) or P6(4), with unit-cell parameters a = 113.62, c = 86.85 A, contain two to five copies of the protein in the asymmetric unit and diffract X-rays to 1.25 A resolution.
Makris N, Hodge SM, Haselgrove C, Kennedy DN, Dale A, Fischl B, Rosen BR, Harris G, Caviness VS, Schmahmann JD. Human cerebellum: surface-assisted cortical parcellation and volumetry with magnetic resonance imaging. J Cogn Neurosci. 2003;15 (4) :584-99.Abstract
We describe a system of surface-assisted parcellation (SAP) of the human cerebellar cortex derived from neural systems functional and behavioral anatomy. This system is based on MRI and preserves the unique morphologic and topographic features of the individual cerebellum. All major fissures of the cerebellum were identified and traced in the flattened representation of the cerebellar cortex using the program "FreeSurfer." Parcellation of the cerebellar cortex followed using the fissure information in conjunction with landmarks using the program "Cardviews" to create 64 gyral-based cerebellar parcellation units. Computer-assisted algorithms enable the execution of the cerebellar parcellation procedure as well as volumetric measurements and topographic localization. The SAP technique makes it possible to represent multimodal structural and functional imaging data on the flattened surface of the cerebellar cortex as illustrated in one functional MRI experiment.
Takeoka M, Kim F, Caviness VS, Kennedy DN, Makris N, Holmes GL. MRI volumetric analysis in rasmussen encephalitis: a longitudinal study. Epilepsia. 2003;44 (2) :247-51.Abstract
PURPOSE: Rasmussen encephalitis is a progressive inflammatory process with difficult-to-control focal or lateralized seizure activity, leading to hemispheric dysfunction and atrophy in advanced stages. Anatomic changes of atrophy may be subtle in earlier phases of the disease, and progressive changes on serial scans may be difficult to detect. We report a case of early-stage Rasmussen encephalitis with a relatively stable clinical course in whom we performed magnetic resonance imaging (MRI)-based volumetric analysis over an interval of 1 year, to assess for volumetric changes. METHODS: Volumetric analysis was performed on two successive MRI scans obtained at age 5 and 6 years, by using the CARDVIEWS program (J Cogn Neurosci, 1996). The images were segmented into gray- and white-matter structures according to signal intensity of their borders semiautomatically, with manual corrections. The cerebral cortex was further subdivided into smaller parcellation units according to anatomic landmarks identifiable on MRI. RESULTS: Stable left cerebral hemispheric atrophy and progressive atrophy in the left precentral gyrus, left inferior frontal gyrus, and left cerebellar atrophy were detected over the 1-year interval. CONCLUSIONS: Volumetric analysis enables early detection and quantification of anatomic changes, identification of focal involvement, and assists in determining the severity of disease and timing for surgical interventions such as hemispherectomy.
Rauch SL, Phillips KA, Segal E, Makris N, Shin LM, Whalen PJ, Jenike MA, Caviness VS, Kennedy DN. A preliminary morphometric magnetic resonance imaging study of regional brain volumes in body dysmorphic disorder. Psychiatry Res. 2003;122 (1) :13-9.Abstract
Morphometric magnetic resonance imaging (MRI) was used to compare regional brain volumes in eight women with body dysmorphic disorder (BDD) and eight healthy comparison subjects. The BDD group exhibited a relative leftward shift in caudate asymmetry and greater total white matter vs. the comparison group. Findings with respect to the caudate nucleus are consistent with both the conceptualization of BDD as an obsessive-compulsive spectrum disorder, and the 'striatal topography model' of obsessive-compulsive disorders.
Rauch SL, Shin LM, Segal E, Pitman RK, Carson MA, McMullin K, Whalen PJ, Makris N. Selectively reduced regional cortical volumes in post-traumatic stress disorder. Neuroreport. 2003;14 (7) :913-6.Abstract
Different subterritories of anterior cingulate cortex (ACC) and adjacent ventromedial frontal cortex have been shown to serve distinct functions. This scheme has influenced contemporary pathophysiologic models of psychiatric disorders. Prevailing neurocircuitry models of post-traumatic stress disorder (PTSD) implicate dysfunction within pregenual ACC and subcallosal cortex (SC), as well as amygdala and hippocampus. In the current study, cortical parcellation of magnetic resonance imaging data was performed to test for volumetric differences in pregenual ACC and SC, between women with PTSD and trauma-exposed women without PTSD. The PTSD group exhibited selectively decreased pregenual ACC and SC volumes. These results are consistent with contemporary schemes regarding functional and structural dissection of frontal cortex, and suggest specific regional cortical pathology in PTSD.

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