Publications by Year: 2011

Kapur T, Tempany CM, Jolesz FA. Proceedings of the 4th Image Guided Therapy Workshop. Image Guided Therapy Workshop. 2011;4 :1-121. 2011 IGT Workshop Proceedings
O'Donnell LJ, Westin C-F. An Introduction to Diffusion Tensor Image Analysis. Neurosurg Clin N Am. 2011;22 (2) :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.

Oguro S, Tuncali K, Elhawary H, Morrison PR, Hata N, Silverman SG. Image registration of pre-procedural MRI and intra-procedural CT images to aid CT-guided percutaneous cryoablation of renal tumors. Int J Comput Assist Radiol Surg. 2011;6 (1) :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'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.
Sandhu R, Dambreville S, Yezzi A, Tannenbaum A. A nonrigid kernel-based framework for 2D-3D pose estimation and 2D image segmentation. IEEE Trans Pattern Anal Mach Intell. 2011;33 (6) :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'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.
Wang X, Grimson EWL, Westin C-F. Tractography segmentation using a hierarchical Dirichlet processes mixture model. Neuroimage. 2011;54 (1) :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.
Yuan J, Madore B, Panych LP. Fat-water selective excitation in balanced steady-state free precession using short spatial-spectral RF pulses. J Magn Reson. 2011;208 (2) :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.
Golby AJ, Kindlmann G, Norton I, Yarmarkovich A, Pieper S, Kikinis R. Interactive diffusion tensor tractography visualization for neurosurgical planning. Neurosurgery. 2011;68 (2) :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.
Jolesz FA. Intraoperative imaging in neurosurgery: where will the future take us?. Acta Neurochir Suppl. 2011;109 :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's Hospital'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).
Elhawary H, Liu H, Patel P, Norton I, Rigolo L, Papademetris X, Hata N, Golby AJ. Intraoperative real-time querying of white matter tracts during frameless stereotactic neuronavigation. Neurosurgery. 2011;68 (2) :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.
Tan H, Hoge SW, Hamilton CA, Günther M, Kraft RA. 3D GRASE PROPELLER: improved image acquisition technique for arterial spin labeling perfusion imaging. Magn Reson Med. 2011;66 (1) :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 × 3 × 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.
Mei C-S, Panych LP, Yuan J, McDannold NJ, Treat LH, Jing Y, Madore B. Combining two-dimensional spatially selective RF excitation, parallel imaging, and UNFOLD for accelerated MR thermometry imaging. Magn Reson Med. 2011;66 (1) :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°C, while maintaining accurate temperature measurements (mean difference between measurements, as observed in gel = 0.1°C ± 0.6; R = 0.98; P > 0.05).
Jing Y, Tao M, Clement GT. Evaluation of a wave-vector-frequency-domain method for nonlinear wave propagation. J Acoust Soc Am. 2011;129 (1) :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'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.
Su H, Camilo A, Cole GA, Hata N, Tempany CM, Fischer GS. High-field MRI-compatible needle placement robot for prostate interventions. Stud Health Technol Inform. 2011;163 :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.
Fennessy FM, Kong CY, Tempany CM, Swan SJ. Quality-of-life assessment of fibroid treatment options and outcomes. Radiology. 2011;259 (3) :785-92.Abstract
PURPOSE: To obtain utilities (a unit of measure of a person'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:
Langs G, Lashkari D, Sweet A, Tie Y, Rigolo L, Golby AJ, Golland P. Learning an atlas of a cognitive process in its functional geometry. Inf Process Med Imaging. 2011;22 :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.
Wassermann D, Rathi Y, Bouix S, Kubicki M, Kikinis R, Shenton M, Westin C-F. White matter bundle registration and population analysis based on Gaussian processes. Inf Process Med Imaging. 2011;22 :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' 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.
Kikinis R, Pieper S. 3D Slicer as a tool for interactive brain tumor segmentation. Conf Proc IEEE Eng Med Biol Soc. 2011;2011 :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.
Zinn PO, Mahajan B, Majadan B, Sathyan P, Singh SK, Majumder S, Jolesz FA, Colen RR. Radiogenomic mapping of edema/cellular invasion MRI-phenotypes in glioblastoma multiforme. PLoS One. 2011;6 (10) :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<0.001). High POSTN and low miR-219 expression were significantly associated with the mesenchymal GBM subtype (P<0.0001). CONCLUSION: Here, we propose a novel diagnostic method to screen for molecular cancer subtypes and genomic correlates of cellular invasion. Our findings also have potential therapeutic significance since successful molecular inhibition of invasion will improve therapy and patient survival in GBM.
Paltiel HJ, Padua HM, Gargollo PC, Cannon GM, Alomari AI, Yu R, Clement GT. Contrast-enhanced, Real-time Volumetric Ultrasound Imaging of Tissue Perfusion: Preliminary Results in a Rabbit Model of Testicular Torsion. Phys Med Biol. 2011;56 (7) :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® before and after unilateral testicular torsion and contralateral orchiopexy. The degree of torsion was 0° in 4 (sham surgery), 180° in 4, 360° in 4, 540° in 4, and 720° 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 'gold standard'. This method is of potential utility in the clinical evaluation of testicular and other organ perfusion.

Rigolo L, Stern E, Deaver P, Golby AJ, Mukundan S. Development of a Clinical Functional Magnetic Resonance Imaging Service. Neurosurg Clin N Am. 2011;22 (2) :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.