Publications by Year: 2007

2007
Kilian M Pohl, Ron Kikinis, and William M Wells. 2007. “Active mean fields: solving the mean field approximation in the level set framework.” Inf Process Med Imaging, 20, Pp. 26-37.Abstract
We describe a new approach for estimating the posterior probability of tissue labels. Conventional likelihood models are combined with a curve length prior on boundaries, and an approximate posterior distribution on labels is sought via the Mean Field approach. Optimizing the resulting estimator by gradient descent leads to a level set style algorithm where the level set functions are the logarithm-of-odds encoding of the posterior label probabilities in an unconstrained linear vector space. Applications with more than two labels are easily accommodated. The label assignment is accomplished by the Maximum A Posteriori rule, so there are no problems of "overlap" or "vacuum". We test the method on synthetic images with additive noise. In addition, we segment a magnetic resonance scan into the major brain compartments and subcortical structures.
Nobuhiko Hata, Steve Piper, Ferenc A Jolesz, Clare M Tempany, Peter M Black, Shigehiro Morikawa, Horoshi Iseki, Makoto Hashizume, and Ron Kikinis. 2007. “Application of open source image guided therapy software in MR-guided therapies.” Med Image Comput Comput Assist Interv, 10, Pt 1, Pp. 491-8.Abstract

We present software engineering methods to provide free open-source software for MR-guided therapy. We report that graphical representation of the surgical tools, interconnectively with the tracking device, patient-to-image registration, and MRI-based thermal mapping are crucial components of MR-guided therapy in sharing such software. Software process includes a network-based distribution mechanism by multi-platform compiling tool CMake, CVS, quality assurance software DART. We developed six procedures in four separate clinical sites using proposed software engineering and process, and found the proposed method is feasible to facilitate multicenter clinical trial of MR-guided therapies. Our future studies include use of the software in non-MR-guided therapies.

Lauren J O'Donnell and Carl-Fredrik Westin. 2007. “Automatic tractography segmentation using a high-dimensional white matter atlas.” IEEE Trans Med Imaging, 26, 11, Pp. 1562-75.Abstract
We propose a new white matter atlas creation method that learns a model of the common white matter structures present in a group of subjects. We demonstrate that our atlas creation method, which is based on group spectral clustering of tractography, discovers structures corresponding to expected white matter anatomy such as the corpus callosum, uncinate fasciculus, cingulum bundles, arcuate fasciculus, and corona radiata. The white matter clusters are augmented with expert anatomical labels and stored in a new type of atlas that we call a high-dimensional white matter atlas. We then show how to perform automatic segmentation of tractography from novel subjects by extending the spectral clustering solution, stored in the atlas, using the Nystrom method. We present results regarding the stability of our method and parameter choices. Finally we give results from an atlas creation and automatic segmentation experiment. We demonstrate that our automatic tractography segmentation identifies corresponding white matter regions across hemispheres and across subjects, enabling group comparison of white matter anatomy.
Elisabetta Sassaroli and Kullervo Hynynen. 2007. “Cavitation threshold of microbubbles in gel tunnels by focused ultrasound.” Ultrasound Med Biol, 33, 10, Pp. 1651-60.Abstract
The investigation of inertial cavitation in micro-tunnels has significant implications for the development of therapeutic applications of ultrasound such as ultrasound-mediated drug and gene delivery. The threshold for inertial cavitation was investigated using a passive cavitation detector with a center frequency of 1 MHz. Micro-tunnels of various diameters (90 to 800 microm) embedded in gel were fabricated and injected with a solution of Optison(trade mark) contrast agent of concentrations 1.2% and 0.2% diluted in water. An ultrasound pulse of duration 500 ms and center frequency 1.736 MHz was used to insonate the microbubbles. The acoustic pressure was increased at 1-s intervals until broadband noise emission was detected. The pressure threshold at which broadband noise emission was observed was found to be dependent on the diameter of the micro-tunnels, with an average increase of 1.2 to 1.5 between the smallest and the largest tunnels, depending on the microbubble concentration. The evaluation of inertial cavitation in gel tunnels rather than tubes provides a novel opportunity to investigate microbubble collapse in a situation that simulates in vivo blood vessels better than tubes with solid walls do.
Simon DiMaio, Tina Kapur, Kevin Cleary, Stephen Aylward, Peter Kazanzides, Kirby G Vosburgh, Randy Ellis, James Duncan, Keyvan Farahani, Heinz Lemke, Terry Peters, William Bill Lorensen, David Gobbi, John Haller, Laurence Larry Clarke, Stephen Pizer, Russell Taylor, Robert Galloway, Gabor Fichtinger, Nobuhiko Hata, Kimberly Lawson, Clare M Tempany, Ron Kikinis, and Ferenc A Jolesz. 2007. “Challenges in image-guided therapy system design.” Neuroimage, 37 Suppl 1, Pp. S144-51.Abstract

System development for image-guided therapy (IGT), or image-guided interventions (IGI), continues to be an area of active interest across academic and industry groups. This is an emerging field that is growing rapidly: major academic institutions and medical device manufacturers have produced IGT technologies that are in routine clinical use, dozens of high-impact publications are published in well regarded journals each year, and several small companies have successfully commercialized sophisticated IGT systems. In meetings between IGT investigators over the last two years, a consensus has emerged that several key areas must be addressed collaboratively by the community to reach the next level of impact and efficiency in IGT research and development to improve patient care. These meetings culminated in a two-day workshop that brought together several academic and industrial leaders in the field today. The goals of the workshop were to identify gaps in the engineering infrastructure available to IGT researchers, develop the role of research funding agencies and the recently established US-based National Center for Image Guided Therapy (NCIGT), and ultimately to facilitate the transfer of technology among research centers that are sponsored by the National Institutes of Health (NIH). Workshop discussions spanned many of the current challenges in the development and deployment of new IGT systems. Key challenges were identified in a number of areas, including: validation standards; workflows, use-cases, and application requirements; component reusability; and device interface standards. This report elaborates on these key points and proposes research challenges that are to be addressed by a joint effort between academic, industry, and NIH participants.

K Hynynen and G Clement. 2007. “Clinical applications of focused ultrasound-the brain.” Int J Hyperthermia, 23, 2, Pp. 193-202.Abstract
This paper provides a historic and contemporary overview of the use of focused ultrasound for treating brain disorders.
Julien Dauguet, Sharon Peled, Vladimir Berezovskii, Thierry Delzescaux, Simon K Warfield, Richard Born, and Carl-Fredrik Westin. 2007. “Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain.” Neuroimage, 37, 2, Pp. 530-8.Abstract
Since the introduction of diffusion weighted imaging (DWI) as a method for examining neural connectivity, its accuracy has not been formally evaluated. In this study, we directly compared connections that were visualized using injected neural tract tracers (WGA-HRP) with those obtained using in-vivo diffusion tensor imaging (DTI) tractography. First, we injected the tracer at multiple sites in the brain of a macaque monkey; second, we reconstructed the histological sections of the labeled fiber tracts in 3D; third, we segmented and registered the fibers (somatosensory and motor tracts) with the anatomical in-vivo MRI from the same animal; and last, we conducted fiber tracing along the same pathways on the DTI data using a classical diffusion tracing technique with the injection sites as seeds. To evaluate the performance of DTI fiber tracing, we compared the fibers derived from the DTI tractography with those segmented from the histology. We also studied the influence of the parameters controlling the tractography by comparing Dice superimposition coefficients between histology and DTI segmentations. While there was generally good visual agreement between the two methods, our quantitative comparisons reveal certain limitations of DTI tractography, particularly for regions at remote locations from seeds. We have thus demonstrated the importance of appropriate settings for realistic tractography results.
Robert V Mulkern, Steven J Haker, and Stephan E Maier. 2007. “Complimentary aspects of diffusion imaging and fMRI: II. Elucidating contributions to the fMRI signal with diffusion sensitization.” Magn Reson Imaging, 25, 6, Pp. 939-52.Abstract
Tissue water molecules reside in different biophysical compartments. For example, water molecules in the vasculature reside for variable periods of time within arteries, arterioles, capillaries, venuoles and veins, and may be within blood cells or blood plasma. Water molecules outside of the vasculature, in the extravascular space, reside, for a time, either within cells or within the interstitial space between cells. Within these different compartments, different types of microscopic motion that water molecules may experience have been identified and discussed. These range from Brownian diffusion to more coherent flow over the time scales relevant to functional magnetic resonance imaging (fMRI) experiments, on the order of several 10s of milliseconds. How these different types of motion are reflected in magnetic resonance imaging (MRI) methods developed for "diffusion" imaging studies has been an ongoing and active area of research. Here we briefly review the ideas that have developed regarding these motions within the context of modern "diffusion" imaging techniques and, in particular, how they have been accessed in attempts to further our understanding of the various contributions to the fMRI signal changes sought in studies of human brain activation.
Sai Chun Tang, Gregory T Clement, and Kullervo Hynynen. 2007. “A Computer-controlled Ultrasound Pulser-receiver System for Transkull Fluid Detection using a Shear Wave Transmission Technique.” IEEE Trans Ultrason Ferroelectr Freq Control, 54, 9, Pp. 1772-83.Abstract

The purpose of this study was to evaluate the performance of a computer-controlled ultrasound pulser-receiver system incorporating a shear mode technique for transskull fluid detection. The presence of fluid in the sinuses of an ex vivo human skull was examined using a pulse-echo method by transmitting an ultrasound beam through the maxilla bone toward the back wall on the other side of the sinus cavity. The pulser was programmed to generate bipolar pulse trains with 5 cycles at a frequency of 1 MHz, repetition frequency of about 20 Hz, and amplitude of 100 V to drive a 1-MHz piezoelectric transducer. Shear and longitudinal waves in the maxilla bone were produced by adjusting the bone surface incident angle to 45 degrees and 0 degrees, respectively. Computer tomography (CT) scans of the skull were performed to verify the ultrasound experiment. Using the shear mode technique, the echo waveform clearly distinguishes the presence of fluid, and the estimated distance of the ultrasound traveled in the sinus is consistent with the measurement from the CT images. Contrarily, using the longitudinal mode, no detectable back wall echo was observed under the same conditions. As a conclusion, this study demonstrated that the proposed pulser-receiver system with the shear mode technique is promising for transskull fluid detecting, such as mucus in a sinus.

Seung-Schik Yoo, Peter T Hu, Ninad Gujar, Ferenc A Jolesz, and Matthew P Walker. 2007. “A deficit in the ability to form new human memories without sleep.” Nat Neurosci, 10, 3, Pp. 385-92.Abstract
Evidence indicates that sleep after learning is critical for the subsequent consolidation of human memory. Whether sleep before learning is equally essential for the initial formation of new memories, however, remains an open question. We report that a single night of sleep deprivation produces a significant deficit in hippocampal activity during episodic memory encoding, resulting in worse subsequent retention. Furthermore, these hippocampal impairments instantiate a different pattern of functional connectivity in basic alertness networks of the brainstem and thalamus. We also find that unique prefrontal regions predict the success of encoding for sleep-deprived individuals relative to those who have slept normally. These results demonstrate that an absence of prior sleep substantially compromises the neural and behavioral capacity for committing new experiences to memory. It therefore appears that sleep before learning is critical in preparing the human brain for next-day memory formation-a worrying finding considering society's increasing erosion of sleep time.
Gordon Kindlmann, Xavier Tricoche, and Carl-Fredrik Westin. 2007. “Delineating white matter structure in diffusion tensor MRI with anisotropy creases.” Med Image Anal, 11, 5, Pp. 492-502.Abstract
Geometric models of white matter architecture play an increasing role in neuroscientific applications of diffusion tensor imaging, and the most popular method for building them is fiber tractography. For some analysis tasks, however, a compelling alternative may be found in the first and second derivatives of diffusion anisotropy. We extend to tensor fields the notion from classical computer vision of ridges and valleys, and define anisotropy creases as features of locally extremal tensor anisotropy. Mathematically, these are the loci 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 the major 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. The crease extraction algorithm we present generates high-quality polygonal models of crease surfaces, which are further simplified by connected-component analysis. We demonstrate anisotropy creases on measured diffusion MRI data, and visualize them in combination with tractography to confirm their anatomic relevance.
Jochen Von Spiczak, Eigil Samset, Simon DiMaio, Gerhard Reitmayr, Dieter Schmalstieg, Catherina Burghart, and Ron Kikinis. 2007. “Device connectivity for image-guided medical applications.” Stud Health Technol Inform, 125, Pp. 482-4.Abstract
The integration of medical devices with software applications is crucial for image-guided medical applications. This work describes a general device interface that has been designed for high-frequency streaming of multi-modal events, thus providing maximum performance and flexibility for such applications. Several sample applications and performance tests are provided to demonstrate the usability of the concept.
Jan Lesniak, Junichi Tokuda, Ron Kikinis, Catherina Burghart, and Nobuhiko Hata. 2007. “A device guidance method for organ motion compensation in MRI-guided therapy.” Phys Med Biol, 52, 21, Pp. 6427-38.Abstract
Organ motion compensation in image-guided therapy is an active area of research. However, there has been little research on motion tracking and compensation in magnetic resonance imaging (MRI)-guided therapy. In this paper, we present a method to track a moving organ in MRI and control an active mechanical device for motion compensation. The method proposed is based on MRI navigator echo tracking enhanced by Kalman filtering for noise robustness. We also developed an extrapolation scheme to resolve any discrepancies between tracking and device control sampling rates. The algorithm was tested in a simulation study using a phantom and an active mechanical tool holder. We found that the method is feasible to use in a clinical MRI scanner with sufficient accuracy (0.36 mm to 1.51 mm depending on the range of phantom motion) and is robust to noise. The method proposed may be useful in MRI-guided targeted therapy, such as focused ultrasound therapy for a moving organ.
Gordon Kindlmann, Daniel B Ennis, Ross T Whitaker, and Carl-Fredrik Westin. 2007. “Diffusion tensor analysis with invariant gradients and rotation tangents.” IEEE Trans Med Imaging, 26, 11, Pp. 1483-99.Abstract
Guided by empirically established connections between clinically important tissue properties and diffusion tensor parameters, we introduce a framework for decomposing variations in diffusion tensors into changes in shape and orientation. Tensor shape and orientation both have three degrees-of-freedom, spanned by invariant gradients and rotation tangents, respectively. As an initial demonstration of the framework, we create a tunable measure of tensor difference that can selectively respond to shape and orientation. Second, to analyze the spatial gradient in a tensor volume (a third-order tensor), our framework generates edge strength measures that can discriminate between different neuroanatomical boundaries, as well as creating a novel detector of white matter tracts that are adjacent yet distinctly oriented. Finally, we apply the framework to decompose the fourth-order diffusion covariance tensor into individual and aggregate measures of shape and orientation covariance, including a direct approximation for the variance of tensor invariants such as fractional anisotropy.
Andrea UJ Mewes, Lilla Zöllei, Petra S Hüppi, Heidelise Als, Gloria B McAnulty, Terrie E Inder, William M Wells, and Simon K Warfield. 2007. “Displacement of brain regions in preterm infants with non-synostotic dolichocephaly investigated by MRI.” Neuroimage, 36, 4, Pp. 1074-85.Abstract
Regional investigations of newborn MRI are important to understand the appearance and consequences of early brain injury. Previously, regionalization in neonates has been achieved with a Talairach parcellation, using internal landmarks of the brain. Non-synostotic dolichocephaly defines a bi-temporal narrowing of the preterm infant's head caused by pressure on the immature skull. The impact of dolichocephaly on brain shape and regional brain shift, which may compromise the validity of the parcellation scheme, has not yet been investigated. Twenty-four preterm and 20 fullterm infants were scanned at term equivalent. Skull shapes were investigated by cephalometric measurements and population registration. Brain tissue volumes were calculated to rule out brain injury underlying skull shape differences. The position of Talairach landmarks was evaluated. Cortical structures were segmented to determine a positional shift between both groups. The preterm group displayed dolichocephalic head shapes and had similar brain volumes compared to the mesocephalic fullterm group. In preterm infants, Talairach landmarks were consistently positioned relative to each other and to the skull base, but were displaced with regard to the calvarium. The frontal and superior region was enlarged; central and temporal gyri and sulci were shifted comparing preterm and fullterm infants. We found that, in healthy preterm infants, dolichocephaly led to a shift of cortical structures, but did not influence deep brain structures. We concluded that the validity of a Talairach parcellation scheme is compromised and may lead to a miscalculation of regional brain volumes and inconsistent parcel contents when comparing infant populations with divergent head shapes.
Yasutoshi Honda and Nobuhiko Hata. 2007. “Dynamic imaging of swallowing in a seated position using open-configuration MRI.” J Magn Reson Imaging, 26, 1, Pp. 172-6.Abstract
PURPOSE: To assess the feasibility of dynamic MRI of swallowing in a seated position using an open-configuration MRI scanner, and to compare its capacity for motion analysis around the pharyngeal wall with that of videofluorography. MATERIALS AND METHODS: Six healthy individuals (four women and two men, mean age = 31.4 +/- 7.5 years) were examined with an open-configuration MRI system using a fast spoiled gradient-recalled echo (SPGR) sequence. Dynamic imaging was performed while the subjects were in a seated position after they swallowed oral contrast medium from a cup. An oral and maxillofacial radiologist measured the motion of six structures: the hyoid bone (HB), larynx (LX), upper oropharynx (UOP), lower oropharynx (LOP), pharyngoesophageal segment (PES) behind the vocal folds, and upper esophagus (ESO). The measured motions were compared with reported values from videofluorography-based observations. RESULTS: Open-configuration MRI depicted the anatomic structures related to swallowing (lip, tongue, soft palate, mandible, pharynx, HB, LX, and PES), and the course of the mylohyoid muscle (MM). The vertical and anteroposterior displacements of these structures did not differ significantly from those measured by videofluorography. CONCLUSION: Dynamic imaging of swallowing using open-configuration MRI provides image information comparable to that obtained from videofluorography.
SP DiMaio, E Samset, Gregory Fischer, Iulian Iordachita, G Fichtinger, Ferenc A Jolesz, and Clare M Tempany. 2007. “Dynamic MRI scan plane control for passive tracking of instruments and devices.” Med Image Comput Comput Assist Interv, 10, Pt 2, Pp. 50-8.Abstract

This paper describes a novel image-based method for tracking robotic mechanisms and interventional devices during Magnetic Resonance Image (MRI)-guided procedures. It takes advantage of the multi-planar imaging capabilities of MRI to optimally image a set of localizing fiducials for passive motion tracking in the image coordinate frame. The imaging system is servoed to adaptively position the scan plane based on automatic detection and localization of fiducial artifacts directly from the acquired image stream. This closed-loop control system has been implemented using an open-source software framework and currently operates with GE MRI scanners. Accuracy and performance were evaluated in experiments, the results of which are presented here.

Suzanne Tharin and Alexandra J Golby. 2007. “Functional brain mapping and its applications to neurosurgery.” Neurosurgery, 60, 4 Suppl 2, Pp. 185-201; discussion 201-2.Abstract

Functional brain mapping may be useful for both preoperative planning and intraoperative neurosurgical decision making. "Gold standard" functional studies such as direct electrical stimulation and recording are complemented by newer, less invasive techniques such as functional magnetic resonance imaging. Less invasive techniques allow more areas of the brain to be mapped in more subjects (including healthy subjects) more often (including pre- and postoperatively). Expansion of the armamentarium of tools allows convergent evidence from multiple brain mapping techniques to bear on pre- and intraoperative decision making. Functional imaging techniques are used to map motor, sensory, language, and memory areas in neurosurgical patients with conditions as diverse as brain tumors, vascular lesions, and epilepsy. In the future, coregistration of high resolution anatomic and physiological data from multiple complementary sources will be used to plan more neurosurgical procedures, including minimally invasive procedures. Along the way, new insights on fundamental processes such as the biology of tumors and brain plasticity are likely to be revealed.

Seung-Schik Yoo, Jong-Hwan Lee, Heather O'Leary, Vivian Lee, Seh-Eun Choo, and Ferenc A Jolesz. 2007. “Functional magnetic resonance imaging-mediated learning of increased activity in auditory areas.” Neuroreport, 18, 18, Pp. 1915-20.Abstract
Our earlier study indicated that functional magnetic resonance imaging (fMRI)-based detection and feedback of regional cortical activity from the auditory area enabled a group of individuals to increase the level of activation mediated by auditory attention during sound stimulation. The long-term ability to maintain an increased level of cortical activation, extending to a time period of a few weeks, however, has not been investigated. We used real-time fMRI to confirm the utility of fMRI in forming a basis for the regulation of brain function to increase the activation in the auditory areas, and demonstrated that the learned ability could be retained after a 2-week period, with additional involvement of an attention-related neural network.
Silvia Alayón, Richard Robertson, Simon K Warfield, and Juan Ruiz-Alzola. 2007. “A fuzzy system for helping medical diagnosis of malformations of cortical development.” J Biomed Inform, 40, 3, Pp. 221-35.Abstract
Malformations of the cerebral cortex are recognized as a common cause of developmental delay, neurological deficits, mental retardation and epilepsy. Currently, the diagnosis of cerebral cortical malformations is based on a subjective interpretation of neuroimaging characteristics of the cerebral gray matter and underlying white matter. There is no automated system for aiding the observer in making the diagnosis of a cortical malformation. In this paper a fuzzy rule-based system is proposed as a solution for this problem. The system collects the available expert knowledge about cortical malformations and assists the medical observer in arriving at a correct diagnosis. Moreover, the system allows the study of the influence of the various factors that take part in the decision. The evaluation of the system has been carried out by comparing the automated diagnostic algorithm with known case examples of various malformations due to abnormal cortical organization. An exhaustive evaluation of the system by comparison with published cases and a ROC analysis is presented in the paper.

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