@proceedings {956486, title = {Proceedings of the 4th Image Guided Therapy Workshop}, journal = {Image Guided Therapy Workshop}, volume = {4}, year = {2011}, pages = {1-121}, author = {Kapur, Tina and Clare M. Tempany and Ferenc A. Jolesz} } @article {477636, title = {An Introduction to Diffusion Tensor Image Analysis.}, journal = {Neurosurg Clin N Am}, volume = {22}, number = {2}, year = {2011}, month = {2011 Apr}, pages = {185-96}, abstract = {Diffusion tensor magnetic resonance imaging (DTI) is a relatively new technology that is popular for imaging the white matter of the brain. This article provides a basic and broad overview of DTI to enable the reader to develop an intuitive understanding of these types of data, and an awareness of their strengths and weaknesses.}, keywords = {Anisotropy, Axons, Brain Mapping, Color, Diffusion Tensor Imaging, False Negative Reactions, False Positive Reactions, History, 20th Century, History, 21st Century, Humans, Image Processing, Computer-Assisted, Neural Pathways}, issn = {1558-1349}, doi = {10.1016/j.nec.2010.12.004}, author = {O{\textquoteright}Donnell, Lauren J and Westin, Carl-Fredrik} } @article {462211, title = {Image registration of pre-procedural MRI and intra-procedural CT images to aid CT-guided percutaneous cryoablation of renal tumors.}, journal = {Int J Comput Assist Radiol Surg}, volume = {6}, number = {1}, year = {2011}, month = {2011 Jan}, pages = {111-7}, abstract = {PURPOSE: To determine whether a non-rigid registration (NRR) technique was more accurate than a rigid registration (RR) technique when fusing pre-procedural contrast-enhanced MR images to unenhanced CT images during CT-guided percutaneous cryoablation of renal tumors. METHODS: Both RR and NRR were applied retrospectively to 11 CT-guided percutaneous cryoablation procedures performed to treat renal tumors (mean diameter; 23 mm). Pre-procedural contrast-enhanced MR images of the upper abdomen were registered to unenhanced intra-procedural CT images obtained just prior to the ablation. RRs were performed manually, and NRRs were performed using an intensity-based approach with affine and Basis-Spline techniques used for modeling displacement. Registration accuracy for each technique was assessed using the 95\% Hausdorff distance (HD), Fiducial Registration Error (FRE) and the Dice Similarity Coefficient (DSC). Statistical differences were analyzed using a two-sided Student{\textquoteright}s t-test. Time for each registration technique was recorded. RESULTS: Mean 95\% HD (1.7 mm), FRE (1.7 mm) and DSC (0.96) using the NRR technique were significantly better than mean 95\% HD (6.4 mm), FRE (5.0 mm) and DSC (0.88) using the RR technique (P \< 0.05 for each analysis). Mean registration times of NRR and RR techniques were 15.2 and 5.7 min, respectively. CONCLUSIONS: The non-rigid registration technique was more accurate than the rigid registration technique when fusing pre-procedural MR images to intra-procedural unenhanced CT images. The non-rigid registration technique can be used to improve visualization of renal tumors during CT-guided cryoablation procedures.}, keywords = {Aged, Aged, 80 and over, Cryosurgery, Female, Humans, Image Processing, Computer-Assisted, Kidney Neoplasms, Magnetic Resonance Imaging, Male, Middle Aged, Monitoring, Intraoperative, Preoperative Care, Retrospective Studies, Tomography, X-Ray Computed}, issn = {1861-6429}, doi = {10.1007/s11548-010-0485-9}, author = {Oguro, Sota and Kemal Tuncali and Elhawary, Haytham and Morrison, Paul R and Hata, Nobuhiko and Silverman, Stuart G} } @article {462186, title = {A nonrigid kernel-based framework for 2D-3D pose estimation and 2D image segmentation.}, journal = {IEEE Trans Pattern Anal Mach Intell}, volume = {33}, number = {6}, year = {2011}, month = {2011 Jun}, pages = {1098-115}, abstract = {In this work, we present a nonrigid approach to jointly solving the tasks of 2D-3D pose estimation and 2D image segmentation. In general, most frameworks that couple both pose estimation and segmentation assume that one has exact knowledge of the 3D object. However, under nonideal conditions, this assumption may be violated if only a general class to which a given shape belongs is given (e.g., cars, boats, or planes). Thus, we propose to solve the 2D-3D pose estimation and 2D image segmentation via nonlinear manifold learning of 3D embedded shapes for a general class of objects or deformations for which one may not be able to associate a skeleton model. Thus, the novelty of our method is threefold: first, we present and derive a gradient flow for the task of nonrigid pose estimation and segmentation. Second, due to the possible nonlinear structures of one{\textquoteright}s training set, we evolve the pre-image obtained through kernel PCA for the task of shape analysis. Third, we show that the derivation for shape weights is general. This allows us to use various kernels, as well as other statistical learning methodologies, with only minimal changes needing to be made to the overall shape evolution scheme. In contrast with other techniques, we approach the nonrigid problem, which is an infinite-dimensional task, with a finite-dimensional optimization scheme. More importantly, we do not explicitly need to know the interaction between various shapes such as that needed for skeleton models as this is done implicitly through shape learning. We provide experimental results on several challenging pose estimation and segmentation scenarios.}, keywords = {Algorithms, Artificial Intelligence, Image Enhancement, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Nonlinear Dynamics, Pattern Recognition, Automated, Principal Component Analysis, Software}, issn = {1939-3539}, doi = {10.1109/TPAMI.2010.162}, author = {Sandhu, Romeil and Dambreville, Samuel and Yezzi, Anthony and Tannenbaum, Allen} } @article {462191, title = {Tractography segmentation using a hierarchical Dirichlet processes mixture model.}, journal = {Neuroimage}, volume = {54}, number = {1}, year = {2011}, month = {2011 Jan 1}, pages = {290-302}, abstract = {In this paper, we propose a new nonparametric Bayesian framework to cluster white matter fiber tracts into bundles using a hierarchical Dirichlet processes mixture (HDPM) model. The number of clusters is automatically learned driven by data with a Dirichlet process (DP) prior instead of being manually specified. After the models of bundles have been learned from training data without supervision, they can be used as priors to cluster/classify fibers of new subjects for comparison across subjects. When clustering fibers of new subjects, new clusters can be created for structures not observed in the training data. Our approach does not require computing pairwise distances between fibers and can cluster a huge set of fibers across multiple subjects. We present results on several data sets, the largest of which has more than 120,000 fibers.}, keywords = {Algorithms, Brain Stem, Cerebellum, Computer graphics, Diffusion Tensor Imaging, Humans, Magnetic Resonance Imaging, Models, Neurological, Nerve Fibers, Probability, Statistics, Nonparametric}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2010.07.050}, author = {Wang, Xiaogang and Grimson, W Eric L and Westin, Carl-Fredrik} } @article {462111, title = {Fat-water selective excitation in balanced steady-state free precession using short spatial-spectral RF pulses.}, journal = {J Magn Reson}, volume = {208}, number = {2}, year = {2011}, month = {2011 Feb}, pages = {219-24}, abstract = {Fat suppression is important but challenging in balanced steady-state free precession (bSSFP) acquisitions, for a number of clinical applications. In the present work, the practicality of performing fat-water selective excitations using spatial-spectral (SPSP) RF pulses in bSSFP sequence is examined. With careful pulse design, the overall duration of these SPSP pulses was kept short to minimize detrimental effects on TR, scan time and banding artifact content. Fat-water selective excitation using SPSP pulses was demonstrated in both phantom and human bSSFP imaging at 3T, and compared to results obtained using a two-point Dixon method. The sequence with SPSP pulses performed better than the two-point Dixon method, in terms of scan time and suppression performance. Overall, it is concluded here that SPSP RF pulses do represent a viable option for fat-suppressed bSSFP imaging.}, keywords = {Fats, Humans, Magnetic Resonance Imaging, Normal Distribution, Phantoms, Imaging, Water}, issn = {1096-0856}, doi = {10.1016/j.jmr.2010.11.005}, author = {Yuan, Jing and Madore, Bruno and Panych, Lawrence P.} } @article {462106, title = {Interactive diffusion tensor tractography visualization for neurosurgical planning.}, journal = {Neurosurgery}, volume = {68}, number = {2}, year = {2011}, month = {2011 Feb}, pages = {496-505}, abstract = {BACKGROUND: Diffusion tensor imaging (DTI) infers the trajectory and location of large white matter tracts by measuring the anisotropic diffusion of water. DTI data may then be analyzed and presented as tractography for visualization of the tracts in 3 dimensions. Despite the important information contained in tractography images, usefulness for neurosurgical planning has been limited by the inability to define which are critical structures within the mass of demonstrated fibers and to clarify their relationship to the tumor. OBJECTIVE: To develop a method to allow the interactive querying of tractography data sets for surgical planning and to provide a working software package for the research community. METHODS: The tool was implemented within an open source software project. Echo-planar DTI at 3 T was performed on 5 patients, followed by tensor calculation. Software was developed that allowed the placement of a dynamic seed point for local selection of fibers and for fiber display around a segmented structure, both with tunable parameters. A neurosurgeon was trained in the use of software in < 1 hour and used it to review cases. RESULTS: Tracts near tumor and critical structures were interactively visualized in 3 dimensions to determine spatial relationships to lesion. Tracts were selected using 3 methods: anatomical and functional magnetic resonance imaging-defined regions of interest, distance from the segmented tumor volume, and dynamic seed-point spheres. CONCLUSION: Interactive tractography successfully enabled inspection of white matter structures that were in proximity to lesions, critical structures, and functional cortical areas, allowing the surgeon to explore the relationships between them.}, keywords = {Adult, Brain Neoplasms, Diffusion Tensor Imaging, Female, Humans, Image Interpretation, Computer-Assisted, Male, Middle Aged, Neurosurgery, Software, Young Adult}, issn = {1524-4040}, doi = {10.1227/NEU.0b013e3182061ebb}, author = {Golby, Alexandra J and Kindlmann, Gordon and Norton, Isaiah and Yarmarkovich, Alexander and Pieper, Steven and Kikinis, Ron} } @article {462136, title = {Intraoperative imaging in neurosurgery: where will the future take us?}, journal = {Acta Neurochir Suppl}, volume = {109}, year = {2011}, month = {2011}, pages = {21-5}, abstract = {Intraoperative MRI (ioMRI) dates back to the 1990s and since then has been successfully applied in neurosurgery for three primary reasons with the last one becoming the most significant today: (1) brain shift-corrected navigation, (2) monitoring/controlling thermal ablations, and (3) identifying residual tumor for resection. IoMRI, which today is moving into other applications, including treatment of vasculature and the spine, requires advanced 3T MRI platforms for faster and more flexible image acquisitions, higher image quality, and better spatial and temporal resolution; functional capabilities including fMRI and DTI; non-rigid registration algorithms to register pre- and intraoperative images; non-MRI imaging improvements to continuously monitor brain shift to identify when a new 3D MRI data set is needed intraoperatively; more integration of imaging and MRI-compatible navigational and robot-assisted systems; and greater computational capabilities to handle the processing of data. The Brigham and Women{\textquoteright}s Hospital{\textquoteright}s "AMIGO" suite is described as a setting for progress to continue in ioMRI by incorporating other modalities including molecular imaging. A call to action is made to have other researchers and clinicians in the field of image guided therapy to work together to integrate imaging with therapy delivery systems (such as laser, MRgFUS, endoscopic, and robotic surgery devices).}, keywords = {Brain Diseases, History, 20th Century, History, 21st Century, Humans, Magnetic Resonance Imaging, Monitoring, Intraoperative, Neurosurgical Procedures}, issn = {0065-1419}, doi = {10.1007/978-3-211-99651-5_4}, author = {Jolesz, Ferenc A} } @article {462101, title = {Intraoperative real-time querying of white matter tracts during frameless stereotactic neuronavigation.}, journal = {Neurosurgery}, volume = {68}, number = {2}, year = {2011}, month = {2011 Feb}, pages = {506-16; discussion 516}, abstract = {BACKGROUND: Brain surgery faces important challenges when trying to achieve maximum tumor resection while avoiding postoperative neurological deficits. OBJECTIVE: For surgeons to have optimal intraoperative information concerning white matter (WM) anatomy, we developed a platform that allows the intraoperative real-time querying of tractography data sets during frameless stereotactic neuronavigation. METHODS: Structural magnetic resonance imaging, functional magnetic resonance imaging, and diffusion tensor imaging were performed on 5 patients before they underwent lesion resection using neuronavigation. During the procedure, the tracked surgical tool tip position was transferred from the navigation system to the 3-dimensional Slicer software package, which used this position to seed the WM tracts around the tool tip location, rendering a geometric visualization of these tracts on the preoperative images previously loaded onto the navigation system. The clinical feasibility of this approach was evaluated in 5 cases of lesion resection. In addition, system performance was evaluated by measuring the latency between surgical tool tracking and visualization of the seeded WM tracts. RESULTS: Lesion resection was performed successfully in all 5 patients. The seeded WM tracts close to the lesion and other critical structures, as defined by the functional and structural images, were interactively visualized during the intervention to determine their spatial relationships relative to the lesion and critical cortical areas. Latency between tracking and visualization of tracts was less than a second for a fiducial radius size of 4 to 5 mm. CONCLUSION: Interactive tractography can provide an intuitive way to inspect critical WM tracts in the vicinity of the surgical region, allowing the surgeon to have increased intraoperative WM information to execute the planned surgical resection.}, keywords = {Adult, Brain Neoplasms, Diffusion Tensor Imaging, Female, Humans, Magnetic Resonance Imaging, Male, Monitoring, Intraoperative, Neuronavigation, Software}, issn = {1524-4040}, doi = {10.1227/NEU.0b013e3182036282}, author = {Elhawary, Haytham and Liu, Haiying and Patel, Pratik and Norton, Isaiah and Rigolo, Laura and Papademetris, Xenophon and Hata, Nobuhiko and Golby, Alexandra J} } @article {462081, title = {3D GRASE PROPELLER: improved image acquisition technique for arterial spin labeling perfusion imaging.}, journal = {Magn Reson Med}, volume = {66}, number = {1}, year = {2011}, month = {2011 Jul}, pages = {168-73}, abstract = {Arterial spin labeling is a noninvasive technique that can quantitatively measure cerebral blood flow. While traditionally arterial spin labeling employs 2D echo planar imaging or spiral acquisition trajectories, single-shot 3D gradient echo and spin echo (GRASE) is gaining popularity in arterial spin labeling due to inherent signal-to-noise ratio advantage and spatial coverage. However, a major limitation of 3D GRASE is through-plane blurring caused by T(2) decay. A novel technique combining 3D GRASE and a periodically rotated overlapping parallel lines with enhanced reconstruction trajectory (PROPELLER) is presented to minimize through-plane blurring without sacrificing perfusion sensitivity or increasing total scan time. Full brain perfusion images were acquired at a 3 {\texttimes} 3 {\texttimes} 5 mm(3) nominal voxel size with pulsed arterial spin labeling preparation sequence. Data from five healthy subjects was acquired on a GE 1.5T scanner in less than 4 minutes per subject. While showing good agreement in cerebral blood flow quantification with 3D gradient echo and spin echo, 3D GRASE PROPELLER demonstrated reduced through-plane blurring, improved anatomical details, high repeatability and robustness against motion, making it suitable for routine clinical use.}, keywords = {Cerebrovascular Circulation, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Perfusion Imaging, Reference Standards, Reproducibility of Results, Spin Labels}, issn = {1522-2594}, doi = {10.1002/mrm.22768}, author = {Tan, Huan and Hoge, W. Scott and Hamilton, Craig A and G{\"u}nther, Matthias and Kraft, Robert A.} } @article {462066, title = {Combining two-dimensional spatially selective RF excitation, parallel imaging, and UNFOLD for accelerated MR thermometry imaging.}, journal = {Magn Reson Med}, volume = {66}, number = {1}, year = {2011}, month = {2011 Jul}, pages = {112-22}, abstract = {MR thermometry can be a very challenging application, as good resolution may be needed along spatial, temporal, and temperature axes. Given that the heated foci produced during thermal therapies are typically much smaller than the anatomy being imaged, much of the imaged field-of-view is not actually being heated and may not require temperature monitoring. In this work, many-fold improvements were obtained in terms of temporal resolution and/or 3D spatial coverage by sacrificing some of the in-plane spatial coverage. To do so, three fast-imaging approaches were jointly implemented with a spoiled gradient echo sequence: (1) two-dimensional spatially selective RF excitation, (2) unaliasing by Fourier encoding the overlaps using the temporal dimension (UNFOLD), and (3) parallel imaging. The sequence was tested during experiments with focused ultrasound heating in ex vivo tissue and a tissue-mimicking phantom. Temperature maps were estimated from phase-difference images based on the water proton resonance frequency shift. Results were compared to those obtained from a spoiled gradient echo sequence sequence, using a t-test. Temporal resolution was increased by 24-fold, with temperature uncertainty less than 1{\textdegree}C, while maintaining accurate temperature measurements (mean difference between measurements, as observed in gel = 0.1{\textdegree}C {\textpm} 0.6; R = 0.98; P > 0.05).}, keywords = {Animals, Cattle, Computer Simulation, Magnetic Resonance Imaging, Muscles, Phantoms, Imaging, Sus scrofa, Thermometers, Time Factors, Ultrasonography}, issn = {1522-2594}, doi = {10.1002/mrm.22788}, author = {Mei, Chang-Sheng and Panych, Lawrence P. and Yuan, Jing and McDannold, Nathan J and Treat, Lisa H and Jing, Yun and Madore, Bruno} } @article {462076, title = {Evaluation of a wave-vector-frequency-domain method for nonlinear wave propagation.}, journal = {J Acoust Soc Am}, volume = {129}, number = {1}, year = {2011}, month = {2011 Jan}, pages = {32-46}, abstract = {A wave-vector-frequency-domain method is presented to describe one-directional forward or backward acoustic wave propagation in a nonlinear homogeneous medium. Starting from a frequency-domain representation of the second-order nonlinear acoustic wave equation, an implicit solution for the nonlinear term is proposed by employing the Green{\textquoteright}s function. Its approximation, which is more suitable for numerical implementation, is used. An error study is carried out to test the efficiency of the model by comparing the results with the Fubini solution. It is shown that the error grows as the propagation distance and step-size increase. However, for the specific case tested, even at a step size as large as one wavelength, sufficient accuracy for plane-wave propagation is observed. A two-dimensional steered transducer problem is explored to verify the nonlinear acoustic field directional independence of the model. A three-dimensional single-element transducer problem is solved to verify the forward model by comparing it with an existing nonlinear wave propagation code. Finally, backward-projection behavior is examined. The sound field over a plane in an absorptive medium is backward projected to the source and compared with the initial field, where good agreement is observed.}, keywords = {Acoustics, Algorithms, Computer Simulation, Fourier Analysis, Motion, Nonlinear Dynamics, Numerical Analysis, Computer-Assisted, Pressure, Reproducibility of Results, Sound, Sound Spectrography, Time Factors, Transducers}, issn = {1520-8524}, doi = {10.1121/1.3504705}, author = {Jing, Yun and Tao, Molei and Clement, Greg T} } @article {462071, title = {High-field MRI-compatible needle placement robot for prostate interventions.}, journal = {Stud Health Technol Inform}, volume = {163}, year = {2011}, month = {2011}, pages = {623-9}, abstract = {This paper presents the design of a magnetic resonance imaging (MRI) compatible needle placement system actuated by piezoelectric actuators for prostate brachytherapy and biopsy. An MRI-compatible modular 3 degree-of-freedom (DOF) needle driver module coupled with a 3-DOF x-y-z stage is proposed as a slave robot to precisely deliver radioactive brachytherapy seeds under interactive MRI guidance. The needle driver module provides for needle cannula rotation, needle insertion and cannula retraction to enable the brachytherapy procedure with the preloaded needles. The device mimics the manual physician gesture by two point grasping (hub and base) and provides direct force measurement of needle insertion force by fiber optic force sensors. The fabricated prototype is presented and an experiment with phantom trials in 3T MRI is analyzed to demonstrate the system compatibility.}, keywords = {Brachytherapy, Equipment Design, Equipment Failure Analysis, Humans, Magnetic Resonance Imaging, Male, Micro-Electrical-Mechanical Systems, Needles, Prostatic Neoplasms, Prosthesis Implantation, Punctures, Surgery, Computer-Assisted, User-Computer Interface}, issn = {0926-9630}, author = {Su, Hao and Camilo, Alex and Cole, Gregory A and Hata, Nobuhiko and Tempany, Clare M and Gregory S. Fischer} } @article {462061, title = {Quality-of-life assessment of fibroid treatment options and outcomes.}, journal = {Radiology}, volume = {259}, number = {3}, year = {2011}, month = {2011 Jun}, pages = {785-92}, abstract = {PURPOSE: To obtain utilities (a unit of measure of a person{\textquoteright}s relative preferences for different health states compared with death or worst possible outcome) for uterine fibroids before and after treatment and to measure short-term utilities for the following uterine fibroid treatments: abdominal hysterectomy, magnetic resonance (MR) imaging-guided focused ultrasound surgery, and uterine artery embolization (UAE). MATERIALS AND METHODS: This retrospective study was approved by the institutional review board and was HIPAA compliant. The waiting trade-off (WTO) method, a variation on the time trade-off (TTO) method, is used to obtain utilities for diagnostic procedures on the basis of the fact that people wait longer to avoid noxious tests and/or procedures. The WTO method provides short-term quality of life tolls in terms of quality-adjusted life-weeks by scaling wait times with pre- and posttreatment utilities. Utilities for uterine fibroids before and after treatment were obtained with the TTO method and a visual analog scale (VAS) by using a questionnaire administered by means of a phone interview. WTO wait times were adjusted for quality of life with VAS and TTO utilities and a transformation of VAS. Wait times were compared by using nonparametric tests. The study participants included 62 patients who had undergone abdominal hysterectomy, 74 who had undergone UAE, and 61 who had undergone MR imaging-guided focused ultrasound surgery. RESULTS: Quality of life increased with all treatments. The median WTO wait time was higher for hysterectomy (21.6 weeks) than for UAE or MR imaging-guided focused ultrasound surgery (14.1 weeks for both) (P < .05). Quality-adjusted life-week tolls were smaller when scaled according to TTO than when scaled according to VAS or transformation of VAS. CONCLUSION: Quality of life increased after all fibroid treatments. WTO is feasible for assessing the quality-adjusted morbidity of treatment procedures. SUPPLEMENTAL MATERIAL: http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.11100704/-/DC1.}, keywords = {Adult, Female, Humans, Hysterectomy, Leiomyoma, Magnetic Resonance Imaging, Interventional, Middle Aged, Quality of Life, Questionnaires, Retrospective Studies, Statistics, Nonparametric, Treatment Outcome, Ultrasonic Therapy, Uterine Artery Embolization, Uterine Neoplasms}, issn = {1527-1315}, doi = {10.1148/radiol.11100704}, author = {Fennessy, Fiona M and Kong, Chung Yin and Tempany, Clare M and Swan, J Shannon} } @article {461981, title = {Learning an atlas of a cognitive process in its functional geometry.}, journal = {Inf Process Med Imaging}, volume = {22}, year = {2011}, month = {2011}, pages = {135-46}, abstract = {In this paper we construct an atlas that captures functional characteristics of a cognitive process from a population of individuals. The functional connectivity is encoded in a low-dimensional embedding space derived from a diffusion process on a graph that represents correlations of fMRI time courses. The atlas is represented by a common prior distribution for the embedded fMRI signals of all subjects. The atlas is not directly coupled to the anatomical space, and can represent functional networks that are variable in their spatial distribution. We derive an algorithm for fitting this generative model to the observed data in a population. Our results in a language fMRI study demonstrate that the method identifies coherent and functionally equivalent regions across subjects.}, keywords = {Algorithms, Artificial Intelligence, Brain, Cognition, Computer Simulation, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Information Storage and Retrieval, Magnetic Resonance Imaging, Models, Anatomic, Models, Neurological, Models, Statistical, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique}, issn = {1011-2499}, author = {Langs, Georg and Lashkari, Danial and Sweet, Andrew and Tie, Yanmei and Rigolo, Laura and Golby, Alexandra J and Golland, Polina} } @article {461976, title = {White matter bundle registration and population analysis based on Gaussian processes.}, journal = {Inf Process Med Imaging}, volume = {22}, year = {2011}, month = {2011}, pages = {320-32}, abstract = {This paper proposes a method for the registration of white matter tract bundles traced from diffusion images and its extension to atlas generation, Our framework is based on a Gaussian process representation of tract density maps. Such a representation avoids the need for point-to-point correspondences, is robust to tract interruptions and reconnections and seamlessly handles the comparison and combination of white matter tract bundles. Moreover, being a parametric model, this approach has the potential to be defined in the Gaussian processes{\textquoteright} parameter space, without the need for resampling the fiber bundles during the registration process. We use the similarity measure of our Gaussian process framework, which is in fact an inner product, to drive a diffeomorphic registration algorithm between two sets of homologous bundles which is not biased by point-to-point correspondences or the parametrization of the tracts. We estimate a dense deformation of the underlying white matter using the bundles as anatomical landmarks and obtain a population atlas of those fiber bundles. Finally we test our results in several different bundles obtained from in-vivo data.}, keywords = {Algorithms, Brain, Computer Simulation, Diffusion Tensor Imaging, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Models, Biological, Models, Statistical, Nerve Fibers, Myelinated, Normal Distribution, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique}, issn = {1011-2499}, author = {Demian Wassermann and Rathi, Yogesh and Bouix, Sylvain and Kubicki, Marek and Kikinis, Ron and Shenton, Martha and Westin, Carl-Fredrik} } @article {461906, title = {3D Slicer as a tool for interactive brain tumor segmentation.}, journal = {Conf Proc IEEE Eng Med Biol Soc}, volume = {2011}, year = {2011}, month = {2011}, pages = {6982-4}, abstract = {User interaction is required for reliable segmentation of brain tumors in clinical practice and in clinical research. By incorporating current research tools, 3D Slicer provides a set of interactive, easy to use tools that can be efficiently used for this purpose. One of the modules of 3D Slicer is an interactive editor tool, which contains a variety of interactive segmentation effects. Use of these effects for fast and reproducible segmentation of a single glioblastoma from magnetic resonance imaging data is demonstrated. The innovation in this work lies not in the algorithm, but in the accessibility of the algorithm because of its integration into a software platform that is practical for research in a clinical setting.}, keywords = {Algorithms, Automation, Brain, Brain Neoplasms, Computer graphics, Computers, Glioblastoma, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Software, User-Computer Interface}, issn = {1557-170X}, doi = {10.1109/IEMBS.2011.6091765}, author = {Kikinis, Ron and Pieper, Steve} } @article {461936, title = {Radiogenomic mapping of edema/cellular invasion MRI-phenotypes in glioblastoma multiforme.}, journal = {PLoS One}, volume = {6}, number = {10}, year = {2011}, month = {2011}, pages = {e25451}, abstract = {BACKGROUND: Despite recent discoveries of new molecular targets and pathways, the search for an effective therapy for Glioblastoma Multiforme (GBM) continues. A newly emerged field, radiogenomics, links gene expression profiles with MRI phenotypes. MRI-FLAIR is a noninvasive diagnostic modality and was previously found to correlate with cellular invasion in GBM. Thus, our radiogenomic screen has the potential to reveal novel molecular determinants of invasion. Here, we present the first comprehensive radiogenomic analysis using quantitative MRI volumetrics and large-scale gene- and microRNA expression profiling in GBM. METHODS: Based on The Cancer Genome Atlas (TCGA), discovery and validation sets with gene, microRNA, and quantitative MR-imaging data were created. Top concordant genes and microRNAs correlated with high FLAIR volumes from both sets were further characterized by Kaplan Meier survival statistics, microRNA-gene correlation analyses, and GBM molecular subtype-specific distribution. RESULTS: The top upregulated gene in both the discovery (4 fold) and validation (11 fold) sets was PERIOSTIN (POSTN). The top downregulated microRNA in both sets was miR-219, which is predicted to bind to POSTN. Kaplan Meier analysis demonstrated that above median expression of POSTN resulted in significantly decreased survival and shorter time to disease progression (P, keywords = {Adult, Aged, Brain Neoplasms, Edema, Female, Gene Expression Profiling, Genomics, Glioblastoma, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, MicroRNAs, Middle Aged, Neoplasm Invasiveness, Phenotype, Software, Survival Analysis}, issn = {1932-6203}, doi = {10.1371/journal.pone.0025451}, author = {Zinn, Pascal O and Mahajan, Bhanu and Majadan, Bhanu and Sathyan, Pratheesh and Singh, Sanjay K and Majumder, Sadhan and Jolesz, Ferenc A and Colen, Rivka R} } @article {462041, title = {Contrast-enhanced, Real-time Volumetric Ultrasound Imaging of Tissue Perfusion: Preliminary Results in a Rabbit Model of Testicular Torsion.}, journal = {Phys Med Biol}, volume = {56}, number = {7}, year = {2011}, month = {2011 Apr 7}, pages = {2183-97}, abstract = {Contrast-enhanced ultrasound (US) imaging is potentially applicable to the clinical investigation of a wide variety of perfusion disorders. Quantitative analysis of perfusion is not widely performed, and is limited by the fact that data are acquired from a single tissue plane, a situation that is unlikely to accurately reflect global perfusion. Real-time perfusion information from a tissue volume in an experimental rabbit model of testicular torsion was obtained with a two-dimensional matrix phased array US transducer. Contrast-enhanced imaging was performed in 20 rabbits during intravenous infusion of the microbubble contrast agent Definity{\textregistered} before and after unilateral testicular torsion and contralateral orchiopexy. The degree of torsion was 0{\textdegree} in 4 (sham surgery), 180{\textdegree} in 4, 360{\textdegree} in 4, 540{\textdegree} in 4, and 720{\textdegree} in 4. An automated technique was developed to analyze the time history of US image intensity in experimental and control testes. Comparison of mean US intensity rate of change and of ratios between mean US intensity rate of change in experimental and control testes demonstrated good correlation with testicular perfusion and mean perfusion ratios obtained with radiolabeled microspheres, an accepted {\textquoteright}gold standard{\textquoteright}. This method is of potential utility in the clinical evaluation of testicular and other organ perfusion.}, keywords = {Animals, Blood Circulation, Contrast Media, Disease Models, Animal, Male, Rabbits, Spermatic Cord Torsion, Time Factors}, issn = {1361-6560}, doi = {10.1088/0031-9155/56/7/018}, author = {Paltiel, H J and Padua, H M and Gargollo, P C and Cannon, G M and Alomari, A I and Yu, R and Clement, G T} } @article {462016, title = {Development of a Clinical Functional Magnetic Resonance Imaging Service.}, journal = {Neurosurg Clin N Am}, volume = {22}, number = {2}, year = {2011}, month = {2011 Apr}, pages = {307-14}, abstract = {One of the limitations of anatomy-based imaging approaches is its relative inability to identify whether specific brain functions may be compromised by the location of brain lesions or contemplated brain surgeries. Of the many techniques available to the surgeon, functional magnetic resonance imaging (fMRI) has become the primary modality of choice because of the ability of MRI to serve as a "one-stop shop" for assessing both anatomy and functionality of the brain. This article discusses the specific requirements for establishing an fMRI program, including specific software and hardware requirements. In addition, the nature of the fMRI CPT codes is discussed.}, keywords = {Brain Mapping, Brain Neoplasms, Education, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Neurosurgical Procedures, Oxygen, Personnel, Hospital, Radiology Department, Hospital, Societies, Medical, Software}, issn = {1558-1349}, doi = {10.1016/j.nec.2011.01.001}, author = {Rigolo, Laura and Stern, Emily and Deaver, Pamela and Golby, Alexandra J and Mukundan, Srinivasan} } @article {461931, title = {Distance Measurement in Middle Ear Surgery using a Telemanipulator.}, journal = {Med Image Comput Comput Assist Interv}, volume = {14}, number = {Pt 1}, year = {2011}, month = {2011}, pages = {41-8}, abstract = {In this article, a new tool for the intraoperative measurement of distances within the middle ear by means of a micromanipulator is presented. The purpose of this work was to offer the surgeon a highly accurate tool for measuring the distances between two points in the 3D operational field. The tool can be useful in various operations; this article focuses, however, on measuring the distance between the stapes footplate and the long process of the incus of the middle ear. This distance is important for estimating the proper prosthesis length in stapedotomy for treating otosclerosis. We evaluated the system using a simplified mechanical model. Our results show that the system can measure distances with a maximum error of 0.04 mm.}, keywords = {Ear, Middle, Electronics, Equipment Design, Humans, Imaging, Three-Dimensional, Micromanipulation, Otosclerosis, Phantoms, Imaging, Reference Values, Reproducibility of Results, Software, Surgery, Computer-Assisted, Telemedicine}, author = {Maier, Thomas and Strauss, Gero and Bauer, Franz and Grasser, Andreas and Hata, Nobuhiko and Lueth, Tim C} } @article {462001, title = {An Empirical Investigation of Motion Effects in eMRI of Interictal Epileptiform Spikes.}, journal = {Magn Reson Imaging}, volume = {29}, number = {10}, year = {2011}, month = {2011 Dec}, pages = {1401-9}, abstract = {We recently developed a functional neuroimaging technique called encephalographic magnetic resonance imaging (eMRI). Our method acquires rapid single-shot gradient-echo echo-planar MRI (repetition time=47 ms); it attempts to measure an MR signal more directly linked to neuronal electromagnetic activity than existing methods. To increase the likelihood of detecting such an MR signal, we recorded concurrent MRI and scalp electroencephalography (EEG) during fast (20-200 ms), localized, high-amplitude (\>50 μV on EEG) cortical discharges in a cohort of focal epilepsy patients. Seen on EEG as interictal spikes, these discharges occur in between seizures and induced easily detectable MR magnitude and phase changes concurrent with the spikes with a lag of milliseconds to tens of milliseconds. Due to the time scale of the responses, localized changes in blood flow or hemoglobin oxygenation are unlikely to cause the MR signal changes that we observed. While the precise underlying mechanisms are unclear, in this study, we empirically investigate one potentially important confounding variable - motion. Head motion in the scanner affects both EEG and MR recording. It can produce brief "spike-like" artifacts on EEG and induce large MR signal changes similar to our interictal spike-related signal changes. In order to explore the possibility that interictal spikes were associated with head motions (although such an association had never been reported), we had previously tracked head position in epilepsy patients during interictal spikes and explicitly demonstrated a lack of associated head motion. However, that study was performed outside the MR scanner, and the root-mean-square error in the head position measurement was 0.7 mm. The large inaccuracy in this measurement therefore did not definitively rule out motion as a possible signal generator. In this study, we instructed healthy subjects to make deliberate brief (\<500 ms) head motions inside the MR scanner and imaged these head motions with concurrent EEG and MRI. We compared these artifactual MR and EEG data to genuine interictal spikes. While per-voxel MR and per-electrode EEG time courses for the motion case can mimic the corresponding time courses associated with a genuine interictal spike, head motion can be unambiguously differentiated from interictal spikes via scalp EEG potential maps. Motion induces widespread changes in scalp potential, whereas interictal spikes are localized and have a regional fall-off in amplitude. These findings make bulk head motion an unlikely generator of the large spike-related MR signal changes that we had observed. Further work is required to precisely identify the underlying mechanisms.}, keywords = {Adult, Algorithms, Artifacts, Echo-Planar Imaging, Electroencephalography, Epilepsy, Female, Head Movements, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Reproducibility of Results, Sensitivity and Specificity, Young Adult}, issn = {1873-5894}, doi = {10.1016/j.mri.2011.03.007}, author = {Sundaram, Padmavathi and Mulkern, Robert V. and Wells III, William M and Triantafyllou, Christina and Loddenkemper, Tobias and Bubrick, Ellen J and Orbach, Darren B} } @article {461926, title = {Estimation of delivered dose in radiotherapy: the influence of registration uncertainty.}, journal = {Med Image Comput Comput Assist Interv}, volume = {14}, number = {Pt 1}, year = {2011}, month = {2011}, pages = {548-55}, abstract = {We present a probabilistic framework to estimate the accumulated radiation dose and the corresponding dose uncertainty that is delivered to important anatomical structures, e.g. the primary tumor and healthy surrounding organs, during radiotherapy. The dose uncertainty we report is a direct result of uncertainties in the estimates of the deformation which aligns the daily cone-beam CT images with the planning CT. The accumulated radiation dose is an important measure to monitor during treatment, in particular to see if it significantly deviates from the planned dose which might indicate that either the patient was not properly positioned before treatment or that the anatomy has changed due to the treatment. In the case of the latter, the treatment plan should be adaptively changed to align with the current patient anatomy. We estimate the accumulated dose distribution, and its uncertainty, retrospectively on a dataset acquired during treatment of cancer in the neck and show the dose distributions in the form of dose volume histograms.}, keywords = {Algorithms, Cone-Beam Computed Tomography, Dose-Response Relationship, Radiation, Elasticity, Humans, Image Processing, Computer-Assisted, Models, Anatomic, Models, Statistical, Probability, Radiometry, Radiotherapy, Radiotherapy Planning, Computer-Assisted, Radiotherapy, Intensity-Modulated, Reproducibility of Results, Tomography, X-Ray Computed}, author = {Risholm, Petter and Balter, James and Wells III, William M} } @article {462121, title = {Evaluation of colonoscopy technical skill levels by use of an objective kinematic-based system.}, journal = {Gastrointest Endosc}, volume = {73}, number = {2}, year = {2011}, month = {2011 Feb}, pages = {315-21}, abstract = {BACKGROUND: Colonoscopy requires training and experience to ensure accuracy and safety. Currently, no objective, validated process exists to determine when an endoscopist has attained technical competence. Kinematics data describing movements of laparoscopic instruments have been used in surgical skill assessment to define expert surgical technique. We have developed a novel system to record kinematics data during colonoscopy and quantitatively assess colonoscopist performance. OBJECTIVE: To use kinematic analysis of colonoscopy to quantitatively assess endoscopic technical performance. DESIGN: Prospective cohort study. SETTING: Tertiary-care academic medical center. POPULATION: This study involved physicians who perform colonoscopy. INTERVENTION: Application of a kinematics data collection system to colonoscopy evaluation. MAIN OUTCOME MEASUREMENTS: Kinematics data, validated task load assessment instrument, and technical difficulty visual analog scale. RESULTS: All 13 participants completed the colonoscopy to the terminal ileum on the standard colon model. Attending physicians reached the terminal ileum quicker than fellows (median time, 150.19 seconds vs 299.86 seconds; p\<.01) with reduced path lengths for all 4 sensors, decreased flex (1.75 m vs 3.14 m; P=.03), smaller tip angulation, reduced absolute roll, and lower curvature of the endoscope. With performance of attending physicians serving as the expert reference standard, the mean kinematic score increased by 19.89 for each decrease in postgraduate year (P\<.01). Overall, fellows experienced greater mental, physical, and temporal demand than did attending physicians. LIMITATION: Small cohort size. CONCLUSION: Kinematic data and score calculation appear useful in the evaluation of colonoscopy technical skill levels. The kinematic score appears to consistently vary by year of training. Because this assessment is nonsubjective, it may be an improvement over current methods for determination of competence. Ongoing studies are establishing benchmarks and characteristic profiles of skill groups based on kinematics data.}, keywords = {Biomechanical Phenomena, Clinical Competence, Colonoscopes, Colonoscopy, Equipment Design, Female, Humans, Internship and Residency, Male, Reproducibility of Results}, issn = {1097-6779}, doi = {10.1016/j.gie.2010.09.005}, author = {Obstein, Keith L and Patil, Vaibhav D and Jayender, Jagadeesan and San Jos{\'e} Est{\'e}par, Ra{\'u}l and Spofford, Inbar S and Lengyel, Balazs I and Kirby G. Vosburgh and Thompson, Christopher C} } @article {462056, title = {Fast Fat-suppressed Reduced Field-of-view Temperature Mapping using 2DRF Excitation Pulses.}, journal = {J Magn Reson}, volume = {210}, number = {1}, year = {2011}, month = {2011 May}, pages = {38-43}, abstract = {The purpose of this study is to develop a fast and accurate temperature mapping method capable of both fat suppression and reduced field-of-view (rFOV) imaging, using a two-dimensional spatially-selective RF (2DRF) pulse. Temperature measurement errors caused by fat signals were assessed, through simulations. An 11{\texttimes}1140μs echo-planar 2DRF pulse was developed and incorporated into a gradient-echo sequence. Temperature measurements were obtained during focused ultrasound (FUS) heating of a fat-water phantom. Experiments both with and without the use of a 2DRF pulse were performed at 3T, and the accuracy of the resulting temperature measurements were compared over a range of TE values. Significant inconsistencies in terms of measured temperature values were observed when using a regular slice-selective RF excitation pulse. In contrast, the proposed 2DRF excitation pulse suppressed fat signals by more than 90\%, allowing good temperature consistency regardless of TE settings. Temporal resolution was also improved, from 12 frames per minute (fpm) with the regular pulse to 28 frames per minute with the rFOV excitation. This technique appears promising toward the MR monitoring of temperature in moving adipose organs, during thermal therapies.}, keywords = {Body Temperature, Body Water, Cheese, Echo-Planar Imaging, Fats, Humans, Image Processing, Computer-Assisted, Models, Theoretical, Phantoms, Imaging, Ultrasonic Therapy}, issn = {1096-0856}, doi = {10.1016/j.jmr.2011.02.004}, author = {Yuan, Jing and Mei, Chang-Sheng and Madore, Bruno and McDannold, Nathan J and Panych, Lawrence P.} } @article {462011, title = {Focused Ultrasound Surgery in Oncology: Overview and Principles.}, journal = {Radiology}, volume = {259}, number = {1}, year = {2011}, month = {2011 Apr}, pages = {39-56}, abstract = {Focused ultrasound surgery (FUS) is a noninvasive image-guided therapy and an alternative to surgical interventions. It presents an opportunity to revolutionize cancer therapy and to affect or change drug delivery of therapeutic agents in new focally targeted ways. In this article the background, principles, technical devices, and clinical cancer applications of image-guided FUS are reviewed.}, keywords = {Humans, Ultrasonic Therapy, Ultrasonography, Interventional}, issn = {1527-1315}, doi = {10.1148/radiol.11100155}, author = {Tempany, Clare M and McDannold, Nathan J and Hynynen, Kullervo and Jolesz, Ferenc A} } @article {462031, title = {Image Registered Gastroscopic Ultrasound (IRGUS) in human subjects: a pilot study to assess feasibility.}, journal = {Endoscopy}, volume = {43}, number = {5}, year = {2011}, month = {2011 May}, pages = {394-9}, abstract = {BACKGROUND AND STUDY AIMS: Endoscopic ultrasound (EUS) is a complex procedure due to the subtleties of ultrasound interpretation, the small field of observation, and the uncertainty of probe position and orientation. Animal studies demonstrated that Image Registered Gastroscopic Ultrasound (IRGUS) is feasible and may be superior to conventional EUS in efficiency and image interpretation. This study explores whether these attributes of IRGUS will be evident in human subjects, with the aim of assessing the feasibility, effectiveness, and efficiency of IRGUS in patients with suspected pancreatic lesions. PATIENTS AND METHODS: This was a prospective feasibility study at a tertiary care academic medical center in human patients with pancreatic lesions on computed tomography (CT) scan. Patients who were scheduled to undergo conventional EUS were randomly chosen to undergo their procedure with IRGUS. Main outcome measures included feasibility, ease of use, system function, validated task load (TLX) assessment instrument, and IRGUS experience questionnaire. RESULTS: Five patients underwent IRGUS without complication. Localization of pancreatic lesions was accomplished efficiently and accurately (TLX temporal demand 3.7 \%; TLX effort 8.6 \%). Image synchronization and registration was accomplished in real time without procedure delay. The mean assessment score for endoscopist experience with IRGUS was positive (66.6 {\textpm} 29.4). Real-time display of CT images in the EUS plane and echoendoscope orientation were the most beneficial characteristics. CONCLUSIONS: IRGUS appears feasible and safe in human subjects, and efficient and accurate at identification of probe position and image interpretation. IRGUS has the potential to broaden the adoption of EUS techniques and shorten EUS learning curves. Clinical studies comparing IRGUS with conventional EUS are ongoing.}, keywords = {Adult, Aged, Aged, 80 and over, Endoscopy, Digestive System, Endosonography, Feasibility Studies, Female, Humans, Image Interpretation, Computer-Assisted, Male, Middle Aged, Pancreatic Diseases, Pilot Projects, Prospective Studies}, issn = {1438-8812}, doi = {10.1055/s-0030-1256241}, author = {Obstein, KL and San Jos{\'e} Est{\'e}par, Ra{\'u}l and Jagadeesan, Jayender and Patil, Vaibhav D and IS Spofford and MB Ryan and Lengyel, Balazs I and R Shams and Kirby G. Vosburgh and Thompson, CC} } @article {462006, title = {Impact of Nonrigid Motion Correction Technique on Pixel-wise Pharmacokinetic Analysis of Free-breathing Pulmonary Dynamic Contrast-enhanced MR Imaging.}, journal = {J Magn Reson Imaging}, volume = {33}, number = {4}, year = {2011}, month = {2011 Apr}, pages = {968-73}, abstract = {PURPOSE: To investigates the impact of nonrigid motion correction on pixel-wise pharmacokinetic analysis of free-breathing DCE-MRI in patients with solitary pulmonary nodules (SPNs). Misalignment of focal lesions due to respiratory motion in free-breathing dynamic contrast-enhanced MRI (DCE-MRI) precludes obtaining reliable time-intensity curves, which are crucial for pharmacokinetic analysis for tissue characterization. MATERIALS AND METHODS: Single-slice 2D DCE-MRI was obtained in 15 patients. Misalignments of SPNs were corrected using nonrigid B-spline image registration. Pixel-wise pharmacokinetic parameters K(trans) , v(e) , and k(ep) were estimated from both original and motion-corrected DCE-MRI by fitting the two-compartment pharmacokinetic model to the time-intensity curve obtained in each pixel. The "goodness-of-fit" was tested with χ(2) -test in pixel-by-pixel basis to evaluate the reliability of the parameters. The percentages of reliable pixels within the SPNs were compared between the original and motion-corrected DCE-MRI. In addition, the parameters obtained from benign and malignant SPNs were compared. RESULTS: The percentage of reliable pixels in the motion-corrected DCE-MRI was significantly larger than the original DCE-MRI (P = 4 {\texttimes} 10(-7) ). Both K(trans) and k(ep) derived from the motion-corrected DCE-MRI showed significant differences between benign and malignant SPNs (P = 0.024, 0.015). CONCLUSION: The study demonstrated the impact of nonrigid motion correction technique on pixel-wise pharmacokinetic analysis of free-breathing DCE-MRI in SPNs.}, keywords = {Adult, Aged, Aged, 80 and over, Computer graphics, Contrast Media, Diagnostic Imaging, Female, Humans, Image Processing, Computer-Assisted, Kinetics, Lung, Magnetic Resonance Imaging, Male, Middle Aged, Motion, Reproducibility of Results, Respiration, User-Computer Interface}, issn = {1522-2586}, doi = {10.1002/jmri.22490}, author = {Tokuda, Junichi and Mamata, Hatsuho and Gill, Ritu R and Hata, Nobuhiko and Kikinis, Ron and Padera, Robert F and Lenkinski, Robert E and Sugarbaker, David J and Hatabu, Hiroto} } @article {462021, title = {Multimodal image registration for preoperative planning and image-guided neurosurgical procedures.}, journal = {Neurosurg Clin N Am}, volume = {22}, number = {2}, year = {2011}, month = {2011 Apr}, pages = {197-206}, abstract = {Image registration is the process of transforming images acquired at different time points, or with different imaging modalities, into the same coordinate system. It is an essential part of any neurosurgical planning and navigation system because it facilitates combining images with important complementary, structural, and functional information to improve the information based on which a surgeon makes critical decisions. Brigham and Women{\textquoteright}s Hospital (BWH) has been one of the pioneers in developing intraoperative registration methods for aligning preoperative and intraoperative images of the brain. This article presents an overview of intraoperative registration and highlights some recent developments at BWH.}, keywords = {Diffusion Magnetic Resonance Imaging, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Neuronavigation, Neurosurgical Procedures, Patient Care Planning, Positron-Emission Tomography, Preoperative Care, Surgery, Computer-Assisted, Uncertainty}, issn = {1558-1349}, doi = {10.1016/j.nec.2010.12.001}, author = {Risholm, Petter and Golby, Alexandra J and Wells III, William M} } @article {462051, title = {Multipathway Sequences for MR Thermometry.}, journal = {Magn Reson Med}, volume = {66}, number = {3}, year = {2011}, month = {2011 Sep}, pages = {658-68}, abstract = {MR-based thermometry is a valuable adjunct to thermal ablation therapies as it helps to determine when lethal doses are reached at the target and whether surrounding tissues are safe from damage. When the targeted lesion is mobile, MR data can further be used for motion-tracking purposes. The present work introduces pulse sequence modifications that enable significant improvements in terms of both temperature-to-noise-ratio properties and target-tracking abilities. Instead of sampling a single magnetization pathway as in typical MR thermometry sequences, the pulse-sequence design introduced here involves sampling at least one additional pathway. Image reconstruction changes associated with the proposed sampling scheme are also described. The method was implemented on two commonly used MR thermometry sequences: the gradient-echo and the interleaved echo-planar imaging sequences. Data from the extra pathway enabled temperature-to-noise-ratio improvements by up to 35\%, without increasing scan time. Potentially of greater significance is that the sampled pathways featured very different contrast for blood vessels, facilitating their detection and use as internal landmarks for tracking purposes. Through improved temperature-to-noise-ratio and lesion-tracking abilities, the proposed pulse-sequence design may facilitate the use of MR-monitored thermal ablations as an effective treatment option even in mobile organs such as the liver and kidneys.}, keywords = {Catheter Ablation, Computer Simulation, Hot Temperature, Humans, Image Processing, Computer-Assisted, Liver, Magnetic Resonance Imaging, Models, Animal, Models, Theoretical, Phantoms, Imaging, Reproducibility of Results, Respiration, Thermography, Time Factors}, issn = {1522-2594}, doi = {10.1002/mrm.22844}, author = {Madore, Bruno and Panych, Lawrence P. and Mei, Chang-Sheng and Yuan, Jing and Chu, Renxin} } @article {461941, title = {Multi-resolution MRI Temperature Monitoring in a Reduced Field of View.}, journal = {Magn Reson Imaging}, volume = {29}, number = {9}, year = {2011}, month = {2011 Nov}, pages = {1205-14}, abstract = {PURPOSE: The purpose was to develop a new magnetic resonance imaging technique for fast temperature monitoring with extended volume\ coverage. MATERIALS AND METHODS: The Multiple Resolutions Along Phase-Encode and Slice-Select Dimensions (MURPS) method was implemented in both a two-dimensional (2D) spoiled gradient echo (SPGR) sequence and a multishot echo-planar imaging (EPI) sequence. Both modified sequences were used to acquire image data from three slices with variable phase-encode resolution and slice thickness. In the SPGR sequence, a 2D resonant frequency pulse was also implemented to enable imaging within a reduced field of view, and this was used to monitor (at 1.5 T) the temperature changes in a live rabbit and in gel phantoms heated by focused ultrasound. A modified EPI sequence was tested during heating of a phantom undergoing motion. RESULTS: The in vivo experiments demonstrated that temperature changes in unexpected locations away from the focal plane, such as near bone structures, could be detected due to the extra volume coverage afforded by the MURPS method. Temperature changes in a moving phantom were resolved using the MURPS EPI sequence with an acquisition rate of three slices every 300 ms. CONCLUSION: The MURPS method enables temperature monitoring over multiple slices without loss of temporal resolution compared with single-slice imaging and, if combined with multishot EPI, enables volume temperature monitoring in moving organs.}, keywords = {Animals, Echo-Planar Imaging, Equipment Design, Gels, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Magnetics, Male, Models, Statistical, Phantoms, Imaging, Rabbits, Temperature, Time Factors, Ultrasonography}, issn = {1873-5894}, doi = {10.1016/j.mri.2011.07.020}, author = {Aljallad, Mohammed H and Yuan, Jing and Pilatou, Magdalini C and McDannold, Nathan J and Panych, Lawrence P.} } @article {462086, title = {The neurosurgical anatomy of the sphenoid sinus and sellar floor in endoscopic transsphenoidal surgery.}, journal = {J Neurosurg}, volume = {114}, number = {5}, year = {2011}, month = {2011 May}, pages = {1319-30}, abstract = {OBJECT: A considerable degree of variability exists in the anatomy of the sphenoid sinus, sella turcica, and surrounding skull base structures. The authors aimed to characterize neuroimaging and intraoperative variations in the sagittal and coronal surgical anatomy of healthy controls and patients with sellar lesions. METHODS: Magnetic resonance imaging studies obtained in 100 healthy adults and 78 patients with sellar lesions were reviewed. The following measurements were made on midline sagittal images: sellar face, sellar prominence, sellar angle, tuberculum sellae angle, sellar-clival angle, length of planum sphenoidale, and length of clivus. The septal configuration of the sphenoid sinus was classified as either simple or complex, according to the number of septa, their symmetry, and their morphological features. The following measurements were made on coronal images: maximum width of the sphenoid sinus and sellar face, and the distance between the parasellar and midclivus internal carotid arteries. Neuroimaging results were correlated with intraoperative findings during endoscopic transsphenoidal surgery. RESULTS: Three sellar floor morphologies were defined in normal adults: prominent (sellar angle of \< 90{\textdegree}) in 25\%, curved (sellar angle 90-150{\textdegree}) in 63\%, flat (sellar angle \> 150{\textdegree}) in 11\%, and no floor (conchal sphenoid) in 1\%. In healthy adults, the following mean measurements were obtained: sellar face, 13.4 mm; sellar prominence, 3.0 mm; sellar angle, 112{\textdegree}; angle of tuberculum sellae, 112{\textdegree}; and sellar-clival angle, 117{\textdegree}. Compared with healthy adults, patients with sellar lesions were more likely to have prominent sellar types (43\% vs 25\%, p = 0.01), a more acute sellar angle (102{\textdegree} vs 112{\textdegree}, p = 0.03), a more prominent sellar floor (3.8 vs 3.0 mm, p \< 0.005), and more acute tuberculum (105{\textdegree} vs 112{\textdegree}, p \< 0.01) and sellar-clival (105{\textdegree} vs 117{\textdegree}, p \< 0.003) angles. A flat sellar floor was more difficult to identify intraoperatively and more likely to require the use of a chisel or drill to expose (75\% vs 25\%, p = 0.01). A simple sphenoid sinus configuration (no septa, 1 vertical septum, or 2 symmetric vertical septa) was noted in 71\% of studies, and the other 29\% showed a complex configuration (2 or more asymmetrical septa, 3 or more septa of any kind, or the presence of a horizontal septum). Intraoperative correlation was more challenging in cases with complex sinus anatomy; the most reliable intraoperative midline markers were the vomer, superior sphenoid rostrum, and bilateral parasellar and clival carotid protuberances. CONCLUSIONS: Preoperative assessment of neuroimaging studies is critical for characterizing the morphological characteristics of the sphenoid sinus, sellar floor, tuberculum sellae, and clivus. The flat sellar type identified in 11\% of people) or a complex sphenoid sinus configuration (in 29\% of people) may make intraoperative correlation substantially more challenging. An understanding of the regional anatomy and its variability can improve the safety and accuracy of transsphenoidal and extended endoscopic skull base approaches.}, keywords = {Adult, Endoscopy, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Neuronavigation, Pituitary Neoplasms, Reference Values, Sella Turcica, Skull Base, Sphenoid Sinus}, issn = {1933-0693}, doi = {10.3171/2010.11.JNS10768}, author = {Zada, Gabriel and Agarwalla, Pankaj K and Mukundan, Srinivasan and Dunn, Ian F and Golby, Alexandra J and Laws, Edward R} } @article {462091, title = {A new metric for detecting change in slowly evolving brain tumors: validation in meningioma patients.}, journal = {Neurosurgery}, volume = {68}, number = {1 Suppl Operative}, year = {2011}, month = {2011 Mar}, pages = {225-33}, abstract = {BACKGROUND: Change detection is a critical component in the diagnosis and monitoring of many slowly evolving pathologies. OBJECTIVE: This article describes a semiautomatic monitoring approach using longitudinal medical images. We test the method on brain scans of patients with meningioma, which experts have found difficult to monitor because the tumor evolution is very slow and may be obscured by artifacts related to image acquisition. METHODS: We describe a semiautomatic procedure targeted toward identifying difficult-to-detect changes in brain tumor imaging. The tool combines input from a medical expert with state-of-the-art technology. The software is easy to calibrate and, in less than 5 minutes, returns the total volume of tumor change in mm. We test the method on postgadolinium, T1-weighted magnetic resonance images of 10 patients with meningioma and compare our results with experts{\textquoteright} findings. We also perform benchmark testing with synthetic data. RESULTS: Our experiments indicated that experts{\textquoteright} visual inspections are not sensitive enough to detect subtle growth. Measurements based on experts{\textquoteright} manual segmentations were highly accurate but also labor intensive. The accuracy of our approach was comparable to the experts{\textquoteright} results. However, our approach required far less user input and generated more consistent measurements. CONCLUSION: The sensitivity of experts{\textquoteright} visual inspection is often too low to detect subtle growth of meningiomas from longitudinal scans. Measurements based on experts{\textquoteright} segmentation are highly accurate but generally too labor intensive for standard clinical settings. We described an alternative metric that provides accurate and robust measurements of subtle tumor changes while requiring a minimal amount of user input.}, keywords = {Brain Neoplasms, Diagnosis, Computer-Assisted, Diagnostic Imaging, Disease Progression, Female, Humans, Longitudinal Studies, Male, Meningeal Neoplasms, Meningioma, Reproducibility of Results, Software, Time Factors}, issn = {1524-4040}, doi = {10.1227/NEU.0b013e31820783d5}, author = {Pohl, Kilian M and Konukoglu, Ender and Novellas, Sebastian and Ayache, Nicholas and Fedorov, Andriy and Talos, Ion-Florin and Golby, Alexandra J and Wells III, William M and Kikinis, Ron and Black, Peter M} } @article {461971, title = {Probabilistic elastography: estimating lung elasticity.}, journal = {Inf Process Med Imaging}, volume = {22}, year = {2011}, month = {2011}, pages = {699-710}, abstract = {We formulate registration-based elastography in a probabilistic framework and apply it to study lung elasticity in the presence of emphysematous and fibrotic tissue. The elasticity calculations are based on a Finite Element discretization of a linear elastic biomechanical model. We marginalize over the boundary conditions (deformation) of the biomechanical model to determine the posterior distribution over elasticity parameters. Image similarity is included in the likelihood, an elastic prior is included to constrain the boundary conditions, while a Markov model is used to spatially smooth the inhomogeneous elasticity. We use a Markov Chain Monte Carlo (MCMC) technique to characterize the posterior distribution over elasticity from which we extract the most probable elasticity as well as the uncertainty of this estimate. Even though registration-based lung elastography with inhomogeneous elasticity is challenging due the problem{\textquoteright}s highly underdetermined nature and the sparse image information available in lung CT, we show promising preliminary results on estimating lung elasticity contrast in the presence of emphysematous and fibrotic tissue.}, keywords = {Data Interpretation, Statistical, Elastic Modulus, Elasticity Imaging Techniques, Emphysema, Humans, Lung, Pulmonary Fibrosis}, issn = {1011-2499}, author = {Risholm, Petter and Ross, James and Washko, George R and Wells III, William M} } @article {461891, title = {Probabilistic Non-rigid Registration of Prostate Images: Modeling and Quantifying Uncertainty}, journal = {Proc IEEE Int Symp Biomed Imaging}, volume = {2011}, year = {2011}, month = {2011 Jun 9}, pages = {553-556}, abstract = {Registration of pre- to intra-procedural prostate images needs to handle the large changes in position and shape of the prostate caused by varying rectal filling and patient positioning. We describe a probabilistic method for non-rigid registration of prostate images which can quantify the most probable deformation as well as the uncertainty of the estimated deformation. The method is based on a biomechanical Finite Element model which treats the prostate as an elastic material. We use a Markov Chain Monte Carlo sampler to draw deformation configurations from the posterior distribution. In practice, we simultaneously estimate the boundary conditions (surface displacements) and the internal deformations of our biomechanical model. The proposed method was validated on a clinical MRI dataset with registration results comparable to previously published methods, but with the added benefit of also providing uncertainty estimates which may be important to take into account during prostate biopsy and brachytherapy procedures.}, issn = {1945-7928}, doi = {10.1109/ISBI.2011.5872467}, author = {Risholm, Petter and Fedorov, Andriy and Pursley, Jennifer and Kemal Tuncali and Cormack, Robert and Wells III, William M} } @article {462046, title = {Retrospectively Gated Cardiac Cine Imaging with Temporal and Spatial Acceleration.}, journal = {Magn Reson Imaging}, volume = {29}, number = {4}, year = {2011}, month = {2011 May}, pages = {457-69}, abstract = {Parallel imaging methods are routinely used to accelerate the image acquisition process in cardiac cine imaging. The addition of a temporal acceleration method, whereby k-space is sampled differently for different time frames, has been shown in prior work to improve image quality as compared to parallel imaging by itself. However, such temporal acceleration strategies prove difficult to combine with retrospectively gated cine imaging. The only currently published method to feature such combination, by Hansen et al. [Magn Reson Med 55 (2006) 85-91] tends to be associated with prohibitively long reconstruction times. The goal of the present work was to develop a retrospectively gated cardiac cine method that features both parallel imaging and temporal acceleration, capable of achieving significant acceleration factors on commonly available hardware and associated with reconstruction times short enough for practical use in a clinical context. Seven cardiac patients and a healthy volunteer were recruited and imaged, with acceleration factors of 3.5 or 4.5, using an eight-channel product cardiac array on a 1.5-T system. The prescribed FOV value proved slightly too small in three patients, and one of the patients had a bigemini condition. Despite these additional challenges, good-quality results were obtained for all slices and all patients, with a reconstruction time of 0.98{\textpm}0.07 s per frame, or about 20 s for a 20-frame slice, using a single processor on a single PC. As compared to using parallel imaging by itself, the addition of a temporal acceleration strategy provided much resistance to artifacts.}, keywords = {Algorithms, Artifacts, Case-Control Studies, Heart, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Cine, Myocardium, Software, Time Factors}, issn = {1873-5894}, doi = {10.1016/j.mri.2011.01.003}, author = {Madore, Bruno and Hoge, W. Scott and Chao, Tzu-Cheng and Zientara, Gary P. and Chu, Renxin} } @article {462026, title = {Special surgical considerations for functional brain mapping.}, journal = {Neurosurg Clin N Am}, volume = {22}, number = {2}, year = {2011}, month = {2011 Apr}, pages = {111-32}, abstract = {The development of functional mapping techniques gives neurosurgeons many options for preoperative planning. Integrating functional and anatomic data can inform patient selection and surgical planning and makes functional mapping more accessible than when only invasive studies were available. However, the applications of functional mapping to neurosurgical patients are still evolving. Functional imaging remains complex and requires an understanding of the underlying physiologic and imaging characteristics. Neurosurgeons must be accustomed to interpreting highly processed data. Successful implementation of functional image-guided procedures requires efficient interactions between neurosurgeon, neurologist, radiologist, neuropsychologist, and others, but promises to enhance the care of patients.}, keywords = {Brain, Brain Mapping, Brain Neoplasms, Central Nervous System Vascular Malformations, Diffusion Tensor Imaging, Epilepsy, Humans, Language, Magnetic Resonance Imaging, Magnetoencephalography, Neurosurgical Procedures, Patient Care Planning, Positron-Emission Tomography, Preoperative Care, Reproducibility of Results, Software}, issn = {1558-1349}, doi = {10.1016/j.nec.2011.01.004}, author = {Kekhia, Hussein and Rigolo, Laura and Norton, Isaiah and Golby, Alexandra J} } @article {462036, title = {Statistical Noise Analysis in GRAPPA using a Parametrized Noncentral Chi Approximation Model.}, journal = {Magn Reson Med}, volume = {65}, number = {4}, year = {2011}, month = {2011 Apr}, pages = {1195-206}, abstract = {The characterization of the distribution of noise in the magnitude MR image is a very important problem within image processing algorithms. The Rician noise assumed in single-coil acquisitions has been the keystone for signal-to-noise ratio estimation, image filtering, or diffusion tensor estimation for years. With the advent of parallel protocols such as sensitivity encoding or Generalized Autocalibrated Partially Parallel Acquisitions that allow accelerated acquisitions, this noise model no longer holds. Since Generalized Autocalibrated Partially Parallel Acquisitions reconstructions yield the combination of the squared signals recovered at each receiving coil, noncentral Chi statistics have been previously proposed to model the distribution of noise. However, we prove in this article that this is a weak model due to several artifacts in the acquisition scheme, mainly the correlation existing between the signals obtained at each coil. Alternatively, we propose to model such correlations with a reduction in the number of degrees of freedom of the signal, which translates in an equivalent nonaccelerated system with a minor number of independent receiving coils and, consequently, a lower signal-to-noise ratio. With this model, a noncentral Chi distribution can be assumed for all pixels in the image, whose effective number of coils and effective variance of noise can be explicitly computed in a closed form from the Generalized Autocalibrated Partially Parallel Acquisitions interpolation coefficients. Extensive experiments over both synthetic and in vivo data sets have been performed to show the goodness of fit of out model.}, keywords = {Algorithms, Brain, Computer Simulation, Data Interpretation, Statistical, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Models, Biological, Models, Statistical, Phantoms, Imaging, Reproducibility of Results, Sensitivity and Specificity}, issn = {1522-2594}, doi = {10.1002/mrm.22701}, author = {Aja-Fern{\'a}ndez, Santiago and Trist{\'a}n-Vega, Antonio and Hoge, W. Scott} } @article {461946, title = {On the Use of Gegenbauer Reconstructions for Shock Wave Propagation Modeling.}, journal = {J Acoust Soc Am}, volume = {130}, number = {3}, year = {2011}, month = {2011 Sep}, pages = {1115-24}, abstract = {In therapeutic ultrasound, the presence of shock waves can be significant due to the use of high intensity beams, as well as due to shock formation during inertial cavitation. Although modeling of such strongly nonlinear waves can be carried out using spectral methods, such calculations are typically considered impractical, since accurate calculations often require hundreds or even thousands of harmonics to be considered, leading to prohibitive computational times. Instead, time-domain algorithms which generally utilize Godunov-type finite-difference schemes are commonly used. Although these time domain methods can accurately model steep shock wave fronts, unlike spectral methods they are inherently unsuitable for modeling realistic tissue dispersion relations. Motivated by the need for a more general model, the use of Gegenbauer reconstructions as a postprocess tool to resolve the band-limitations of the spectral methods are investigated. The present work focuses on eliminating the Gibbs phenomenon when representing a steep wave front using a limited number of harmonics. Both plane wave and axisymmetric 2D transducer problems will be presented to characterize the proposed method.}, keywords = {Algorithms, Computer Simulation, Equipment Design, Fourier Analysis, High-Energy Shock Waves, Models, Theoretical, Motion, Numerical Analysis, Computer-Assisted, Pressure, Time Factors, Transducers, Ultrasonics}, issn = {1520-8524}, doi = {10.1121/1.3621485}, author = {Jing, Yun and Clement, Greg T} }