3D Slicer Enabled Research

Publication: Tissue Eng Part C Methods. 2012 Jan 7. PMID: 22224751 | PDF

Authors: Rytlewski JA, Geuss LR, Anyaeji CI, Lewis EW, Suggs L.

Institution: The University of Texas at Austin, Biomedical Engineering, Austin, TX, USA.

Background/Purpose: Morphological analysis is an essential step in verifying the success of a tissue engineering strategy where researchers must determine the presence of a desired cellular phenotype. While morphometry has transitioned from observational grading to computational quantification, established quantitative methods eliminate information by relying on two-dimensional (2D) analysis to describe three-dimensional (3D) niches. In this study, we demonstrate the validity and utility of 3D morphological quantification using two common angiogenesis assays in our fibrin-based in vitro model: (1) the microcarrier bead assay with human mesenchymal stem cells and (2) the rat aortic ring outgrowth assay. The quantification method is based on collecting and segmenting fluorescent confocal z-stacks into 3D models with 3D Slicer, an open-source MRI/CT analysis program. Data from 3D models are then processed into biologically relevant metrics in MATLAB for statistical analysis. Metrics include descriptive parameters such as vascular network length, volume, number of network segments, and degree of network branching. Our results indicate that 2D measures are significantly different than their 3D counterparts unless the vascular network exhibits anisotropic growth along the plane of imaging. Additionally, the statistical outcomes of 3D morphological quantification agreed with our initial qualitative observations among different test groups. This novel quantification approach generates more spatially accurate and objective measures, representing an important step towards improving the reliability of morphological comparisons.

Publication: Anat Rec (Hoboken). 2012 Jan;295(1):132-40. PMID: 22095921

Authors: Greene SJ, Killiany RJ; Alzheimer's Disease Neuroimaging Initiative

Institution: Department of Anatomy and Neurobiology, University of Vermont College of Medicine, Burlington, VT, USA.

Background/Purpose: Atrophy within the hippocampus (HP) as measured by magnetic resonance imaging (MRI) is a promising biomarker for the progression to Alzheimer's disease (AD). Subregions of the HP along the longitudinal axis have been found to demonstrate unique function, as well as undergo differential changes in the progression to AD. Little is known of relationships between such HP subregions and other potential biomarkers, such as neuropsychological (NP), genetic, and cerebral spinal fluid (CSF) beta amyloid and tau measures. The purpose of this study was to subdivide the hippocampus to determine how the head, body, and tail were affected in normal control, mild cognitively impaired, and AD subjects, and investigate relationships with HP subregions and other potential biomarkers. MRI scans of 120 participants of the Alzheimer's Disease Neuroimaging Initiative were processed using FreeSurfer, and the HP was subdivided using 3D Slicer. Each subregion was compared among groups, and correlations were used to determine relationships with NP, genetic, and CSF measures. Results suggest that HP subregions are undergoing differential atrophy in AD, and demonstrate unique relationships with NP and CSF data. Discriminant function analyses revealed that these regions, when combined with NP and CSF measures, were able to classify by diagnostic group, and classify MCI subjects who would and would not progress to AD within 12 months.

Funding:

• AG000277/AG/NIA NIH HHS/United States
• K01 AG030514/AG/NIA NIH HHS/United States
• P30 AG010129/AG/NIA NIH HHS/United States
• U01 AG024904/AG/NIA NIH HHS/United States

Publication: PLoS ONE 6(11): e27372. doi:10.1371/journal.pone.0027372 2011 Nov; | PDF

Authors: Charles F. Caskey, Mario Hlawitschka, Shengping Qin, Lisa M. Mahakian, Robert D. Cardiff, John M. Boone, Katherine W. Ferrara

Institution: Department of Biomedical Engineering, University of California Davis, Davis, California, USA.

Background/Purpose: Therapeutic ultrasound (US) can be noninvasively focused to activate drugs, ablate tumors and deliver drugs beyond the blood brain barrier. However, well-controlled guidance of US therapy requires fusion with a navigational modality, such as magnetic resonance imaging (MRI) or X-ray computed tomography (CT). Here, we developed and validated tissue characterization using a fusion between US and CT. The performance of the CT/US fusion was quantified by the calibration error, target registration error and fiducial registration error. Met-1 tumors in the fat pads of 12 female FVB mice provided a model of developing breast cancer with which to evaluate CT-based tissue segmentation. Hounsfield units (HU) within the tumor and surrounding fat pad were quantified, validated with histology and segmented for parametric analysis (fat: −300 to 0 HU, protein-rich: 1 to 300 HU, and bone: HU>300). Our open source CT/US fusion system differentiated soft tissue, bone and fat with a spatial accuracy of ~1 mm. Region of interest (ROI) analysis of the tumor and surrounding fat pad using a 1 mm² ROI resulted in mean HU of 68±44 within the tumor and −97±52 within the fat pad adjacent to the tumor (p<0.005). The tumor area measured by CT and histology was correlated (r2 = 0.92), while the area designated as fat decreased with increasing tumor size (r2 = 0.51). Analysis of CT and histology images of the tumor and surrounding fat pad revealed an average percentage of fat of 65.3% vs. 75.2%, 36.5% vs. 48.4%, and 31.6% vs. 38.5% for tumors <75 mm³, 75–150 mm³ and >150 mm³, respectively. Further, CT mapped bone-soft tissue interfaces near the acoustic beam during real-time imaging. Combined CT/US is a feasible method for guiding interventions by tracking the acoustic focus within a pre-acquired CT image volume and characterizing tissues proximal to and surrounding the acoustic focus.

Funding:

• NIH R01CA103828

Publication: Am J Obstet Gynecol. 2011 Oct 12. PMID: 22075059

Authors: Rodrigues AA Jr, Bassaly R, McCullough M, Terwilliger HL, Hart S, Downes K, Hoyte L.

Institution: Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics and Gynecology, University of South Florida College of Medicine, Tampa, FL.

Background/Purpose: OBJECTIVE: We describe a new parameter based on magnetic resonance 3-dimensional (3D) reconstructions proposed to evaluate levator ani muscle (LAM) laxity in women with pelvic organ prolapse (POP). STUDY DESIGN: This is an institutional review board-approved, retrospective chart review of 35 women with POP, stages I-IV. The 3D Slicer software package was used to perform 2-dimensional and 3D measurements and the levator ani subtended volume (LASV) was described. Basically, the LASV represents the volume contained by LAM between 2 planes, which coincides with pubococcygeal line and H line. Correlations among measurements, ordinal POP stages, POP Quantification (POPQ) individual measurements, and validated questionnaires were performed. RESULTS: The LASV differentiated major (III and IV) from minor (I and II) POPQ stages, which positively correlated to POP stages and POPQ individual measurements. CONCLUSION: The LASV is a promising parameter to evaluate the LAM laxity.

Publication: Interact Cardiovasc Thorac Surg. 2011 Oct;13(4):453-5. PMID: 21798888 | PDF

Authors: Furák J., Szakács L., Nagy A., Rovó L.

Institution: Department of Oto-Rhino-Laryngology, Head and Neck Surgery, University of Szeged, Szeged, Hungary.

Background/Purpose: After suffering an inhalation burn, a 22-year-old male was intubated for seven days. Full-length massive scar formation in the upper airway necessitated tracheostomy five months later. After this, the stenosis became complete in the cricoid region, and a long cannula was needed to maintain the severely damaged middle-distal trachea. After unsuccessful laser dilatation, the more stenotic 3 cm distal tracheal segment was resected, but two months later the stenosis recurred. As resection was ineffective, tracheoplasty was performed via a right-sided thoracotomy; the re-stenotized trachea was incised in length and successfully extended with 5 cm long, oval-shaped rib cartilage. Three months later, the complete cricotracheal stenosis was fixed by combined laryngofissure and cricoid laminotomy with two 6 cm×2.5 cm cartilage pieces sutured into the incisions. The middle portion of the trachea was expanded with a similar graft inserted into the anterior wall below the tracheostomy. The fixing T-tube was removed three months later, and the patient had an adequate airway two years after the last procedure. We conclude that multiple cartilage graft reconstruction can be successful even after the development of an extremely long airway stenosis following inhalation burn injury.

Publication: Airway Inspector

Contact Person: Raul San Jose Estepar

Institution: Surgical Planning Laboratory at Brigham and Women's Hospital, Boston, MA.

Background/Purpose: Airway Inspector is a free open source tool for CT-based image quantitative analysis of the lung. It provides the tools that clinical scientist can used to explore airway morphology and desitometric characteristics. Airway Inspector is the gateway to phenotype airway diseases. Airway Inspector is maintained by the Applied Chest Imaging Laboratory (ACIL) and is based on the 3D Slicer. The 3D Slicer is a general purposed open source platform for medical image analysis maintained by the Surgical Planning Laboratory at Brigham and Women's Hospital, Boston, MA.

Funding:

• 5K25 HL104085

Publication: IEEE Trans Biomed Eng. 2011 Jul;58(7):2031-7. PMID: 21744085

Authors: Uneri A, Schafer S, Mirota DJ, Nithiananthan S, Otake Y, Taylor RH, Siewerdsen JH.

Institution: Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.

Background/Purpose: A system architecture has been developed for integration of intraoperative 3D imaging [viz., mobile C-arm cone-beam CT (CBCT)] with surgical navigation (e.g., trackers, endoscopy, and preoperative image and planning data). The goal of this paper is to describe the architecture and its handling of a broad variety of data sources in modular tool development for streamlined use of CBCT guidance in application-specific surgical scenarios. METHODS: The architecture builds on two proven open-source software packages, namely the cisst package (Johns Hopkins University, Baltimore, MD) and 3D Slicer (Brigham and Women's Hospital, Boston, MA), and combines data sources common to image-guided procedures with intraoperative 3D imaging. Integration at the software component level is achieved through language bindings to a scripting language (Python) and an object-oriented approach to abstract and simplify the use of devices with varying characteristics. The platform aims to minimize offline data processing and to expose quantitative tools that analyze and communicate factors of geometric precision online. Modular tools are defined to accomplish specific surgical tasks, demonstrated in three clinical scenarios (temporal bone, skull base, and spine surgery) that involve a progressively increased level of complexity in toolset requirements. RESULTS: The resulting architecture (referred to as "TREK") hosts a collection of modules developed according to application-specific surgical tasks, emphasizing streamlined integration with intraoperative CBCT. These include multi-modality image display; 3D-3D rigid and deformable registration to bring preoperative image and planning data to the most up-to-date CBCT; 3D-2D registration of planning and image data to real-time fluoroscopy; infrared, electromagnetic, and video-based trackers used individually or in hybrid arrangements; augmented overlay of image and planning data in endoscopic or in-room video; and real-time "virtual fluoroscopy" computed from GPU-accelerated digitally reconstructed radiographs (DRRs). Application in three preclinical scenarios (temporal bone, skull base, and spine surgery) demonstrates the utility of the modular, task-specific approach in progressively complex tasks. CONCLUSIONS: The design and development of a system architecture for image-guided surgery has been reported, demonstrating enhanced utilization of intraoperative CBCT in surgical applications with vastly different requirements. The system integrates C-arm CBCT with a broad variety of data sources in a modular fashion that streamlines the interface to application-specific tools, accommodates distinct workflow scenarios, and accelerates testing and translation of novel toolsets to clinical use. The modular architecture was shown to adapt to and satisfy the requirements of distinct surgical scenarios from a common code-base, leveraging software components arising from over a decade of effort within the imaging and computer-assisted interventions community.

Publication: IEEE Trans Biomed Eng. 2011 Jul;58(7):2031-7. PMID: 21435970 | PDF

Authors: Caitlin T. Yeo, Tamas Ungi, Paweena U-Thainual, Andras Lasso, Robert C. McGraw, Gabor Fichtinger

Institution: School of Medicine, Queen’s University, Kingston ON K7L 3N6, Canada

Background/Purpose: The purpose of this study was to determine if augmented reality image overlay and laser guidance systems can assist learn how to perform the procedure without the risk of errors medical trainees in learning the correct placement of a needle for causing harm to the patient [2]. Additionally, simulation allows percutaneous facet joint injection. The Perk Station training suite was used to conduct and record the needle insertion procedures. A total of 40 volunteers were randomized into two groups of 20. 1) The Overlay group received a training session that consisted of four insertions with image and laser guidance, followed by two insertions with laser overlay only. 2) The Control group received a training session of six classical freehand insertions. Both groups then conducted two freehand insertions. The movement of the needle was tracked during the series of insertions. The final insertion procedure was assessed to determine if there was a benefit to the overlay method compared to the freehand insertions. The Overlay group had a better success rate (83.3% versus 68.4%, p = 0.002), and potential for less tissue damage as measured by the amount of needle movement inside the phantom (3077.6 mm² versus 5607.9 mm², p = 0.01). These results suggest that an augmented reality overlay guidance system can assist medical trainees in acquiring technical competence in a percutaneous needle insertion procedure.

Funding:

• NIH R01-CA118371
• Ministry of Research and Innovation Ontario Postdoctoral Fellowship

Publication: Int J Med Robot. 2011 Jun;7(2):193-201. PMID: 21538767 | PDF

Authors: Jagadeesan Jayender, Rajni V. Patel, Gregory F. Michaud, Nobuhiko Hata

Institution: Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

Background/Purpose: The preferred method of treatment for atrial fibrillation (AF) is by catheter ablation, in which a catheter is guided into the left atrium through a transseptal puncture. However, the transseptal puncture constrains the catheter, thereby limiting its manoeuvrability and increasing the difficulty in reaching various locations in the left atrium. In this paper, we address the problem of choosing the optimal transseptal puncture location for performing cardiac ablation to obtain maximum manoeuvrability of the catheter. We have employed an optimization algorithm to maximize the global isotropy index (GII) to evaluate the optimal transseptal puncture location. As part of this algorithm, a novel kinematic model for the catheter has been developed, based on a continuum robot model. Pre-operative MR/CT images of the heart are segmented using the open source image-guided therapy software, 3D Slicer, to obtain models of the left atrium and septal wall. These models are input to the optimization algorithm to evaluate the optimal transseptal puncture location.

Funding:

• Intelligent Surgical Instruments Project, METI Grant, Japan

Publication: N Engl J Med. 2011 Mar 10;364(10):897-906. PMID: 21388308 | PDF

Authors: George R. Washko, Gary M. Hunninghake, Isis E. Fernandez, Yuka Okajima, Tsuneo Yamashiro, James C. Ross, Raúl San José Estépar, David A. Lynch, John M. Brehm, Katherine P. Andriole, Alejandro A. Diaz, Ramin Khorasani, Katherine D’Aco, Frank C. Sciurba, Edwin K. Silverman, Hiroto Hatabu, Ivan O. Rosas

Institution: Pulmonary and Critical Care Division, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA

Background/Purpose: Cigarette smoking is associated with emphysema and radiographic interstitial lung abnormalities. The degree to which interstitial lung abnormalities are associated with reduced total lung capacity and the extent of emphysema is not known. We looked for interstitial lung abnormalities in 2416 (96%) of 2508 high-resolution computed tomographic (HRCT) scans of the lung obtained from a cohort of smokers. We used linear and logistic regression to evaluate the associations between interstitial lung abnormalities and HRCT measurements of total lung capacity and emphysema. Quantitative measures of total lung capacity and emphysema were performed with the Airway Inspector, the tool based on 3D Slicer for lung image analysis.

Funding:

• U01 HL089897
• U01 HL089856
• K23 HL089353
• K08 HL092222
• K25 HL104085
• T32 HL07427
• R21CA116271
• K23 HL087030
• Parker B. Francis Foundation

Publication: BMC Medical Imaging 2011 Feb; 11:5. | PDF

Authors: Gianni Frisardi, Giacomo Chessa, Sandro Barone, Alessandro Paoli, Armando Razionale and Flavio Frisardi

Institution: "Epochè" Orofacial Pain Center, Nettuno (Rome), Italy.

Background/Purpose: A precise placement of dental implants is a crucial step to optimize both prosthetic aspects and functional constraints. In this context, the use of virtual guiding systems has been recognized as a fundamental tool to control the ideal implant position. In particular, complex periodontal surgeries can be performed using preoperative planning based on CT data. The critical point of the procedure relies on the lack of accuracy in transferring CT planning information to surgical field through custom-made stereo-lithographic surgical guides. Methods: In this work, a novel methodology is proposed for monitoring loss of accuracy in transferring CT dental information into periodontal surgical field. The methodology is based on integrating 3D data of anatomical (impression and cast) and preoperative (radiographic template) models, obtained by both CT and optical scanning processes. Results: A clinical case, relative to a fully edentulous jaw patient, has been used as test case to assess the accuracy of the various steps concurring in manufacturing surgical guides. In particular, a surgical guide has been designed to place implants in the bone structure of the patient. The analysis of the results has allowed the clinician to monitor all the errors, which have been occurring step by step manufacturing the physical templates. Conclusions: The use of an optical scanner, which has a higher resolution and accuracy than CT scanning, has demonstrated to be a valid support to control the precision of the various physical models adopted and to point out possible error sources. A case study regarding a fully edentulous patient has confirmed the feasibility of the proposed methodology.

Publication: Presented at 62nd Cardiological society of India conference, Kolkata, India. | PDF

Authors: Christopher, J., Mohan Rao MB.,Chary, Duraikannu, Kishore,LT., Krishnam Raju

Institution: Care Hospitals, Hyderabad, India

Background/Purpose: Functional evaluation of coronary arteries involves study of their 3D shapes and diameters. Segmentation of vascular structures from 3D-Computerized Tomographic Angiogram (CTA) images can be achieved by using VMTK. This gives: (1) a polygonal surface model of vascular structures having centerline based geometric quantities and (2) compute centerlines and Maximal Inscribed Sphere Radius (MISR) of branching tubular structures (Voronoi image). VMTK module integrated in Slicer3 is used as it allows use of other Slicer3 modules for processing of images. We use: VesselEnhancement, EasyLevelsetSegmentation and Centerlines modules for study.

Institution: The Initiative in Innovative Computing (IIC), Harvard University, Cambridge, Massachusetts

Project: IIC AstroMed Project

Background/Purpose: While astronomy and medical imaging seem very different, both fields search large amounts of image data looking for meaningful patterns. For example, a physician may inspect a patient's MRI scans looking for signs of disease, while an astronomer will analyze radio telescope image data to find evidence of a new star being born. The two sciences have separately developed many techniques to analyze, visualize, and catalog complex multi-dimensional imaging data, but seldom have experts from the two areas worked together.

The 3D Slicer software package is AstroMed's core tool for astronomical 3D data visualization. Originally designed for medical image analysis, 3D Slicer has many capabilities that are uncommon in astronomy software.

The AstroMed project brings together researchers from the Harvard Medical School and the Harvard-Smithsonian Center for Astrophysics, along with both national and international collaborators, to combine their knowledge and advance the state-of-the-art in both medical imaging and astronomy.

Related article in the February 11, 2011 issue of Science Magazine.

Publication: Biomed Sci Instrum. 2011;47:135-41. PMID: 21525610

Authors: Vatta F, Di Salle F.

Institution: Maastricht University, Maastricht, The Netherlands.

Background/Purpose: Autism spectrum disorders (ASD) are a neurodevelopmental condition with multiple causes, comorbid conditions, and a wide range in the type and severity of symptoms expressed by different individuals. This makes the neuroanatomy of autism inherently difficult to describe. It has been assumed in the scientific literature that deviations in regional brain size in clinical samples are directly related to maldevelopment or pathogenesis. The performed clinical studies analyzed specific brain structures that are assumed to be correlated to autistic brain behaviors. Examples of performed analyses, based upon manual or semi-automated segmentation from magnetic resonance imaging (MRI) scans, include volumetric measures of specific brain structures, or small groups of structures, as caudate, corpus callosum, putamen, hippocampus, nucleus accumbens, evaluating differences between groups of subjects with autism and control subjects. Nonetheless, the brain regions analyzed that differ between patients and control subjects have not been always consistent over the performed studies. This inconsistency might be due to the fact that the specific single volume differences that have been reported in the literature for the different brain structures under investigation may, instead, be not independent during pathogenesis. Hence, this issue comes into play in logically framing a comprehensive assessment of putative abnormalities in regional brain volumes. To this aim, a whole brain investigation system for a semi-automated morphometric statistical analysis of brain anatomy is presented in this paper and validated on a selected group of patients diagnosed with ASD that completed a 1.5 T magnetic resonance image (MRI) of the brain. The proposed system, which is mainly built basing upon the FreeSurfer and the 3D Slicer software frameworks for the volumetric analysis of brain imaging data, lies its foundations on the higher statistical power of the region of interest (ROI) approach, but equally aims at a higher exploratory power as it doesn't restrict its focus to a small number of specific regions, thanks to a whole brain unified approach.

Publication: Neurosurgery. 2011 Apr;68(4):1077-83. PMID: 21242825

Authors: Chen DQ, Quan J, Guha A, Tymianski M, Mikulis D, Hodaie M.

Institution: Division of Neurosurgery, Toronto Western Hospital and University of Toronto, Toronto, Ontario, Canada.

Background/Purpose: Preservation of cranial nerves (CN) is of paramount concern in the treatment of vestibular schwannomas (VS), particularly in large tumors with thinned and distorted CN fibers. However, imaging of the CN fibers surrounding VS has been limited using 2D imaging alone.

OBJECTIVE: We assessed whether tractography of the CN combined with anatomical MR imaging of the tumor can provide superior 3D visualization of tumor/CN complexes.

METHODS: 3T MR imaging including diffusion tensor imaging (DTI) and anatomical images were analyzed in three subjects with VS using 3D Slicer software. The DTI images were used to tract the courses of trigeminal, abducens, facial, and vestibulocochlear nerves. The anatomical images were used to model the 3D volume reconstruction of the tumor. The two sets of images were then superimposed using linear registration.

RESULTS: Combined 3D tumor modelling and cranial nerve tractography can effectively and consistently reconstruct the 3D spatial relationship of CN/tumor complexes, and allows for superior visualization compared with 2D imaging. Lateral and superior distortion of the trigeminal nerve was observed in all cases. The position of the facial nerve was primarily anteriorly and inferiorly. The Gasserian ganglion and early postganglionic branches could also be visualized.

CONCLUSION: Tractography and anatomical imaging were successfully combined to demonstrate the precise location of surrounding CN fibers. This technique can be useful in both neuronavigation and radiosurgical planning. Since knowledge of the course of these fibers is of important clinical interest, implementation of this technique may help decrease injury to cranial nerves during treatment of these lesions.

Publication: Neurosurgery. 2011 Apr;68(4):1077-83. PMID: 21135719

Authors: Elhawary H, Liu H, Patel P, Norton I, Rigolo L, Papademetris X, Hata N, Golby AJ

Institution: Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.

Background/Purpose: Brain surgery faces important challenges when trying to achieve maximum tumor resection while avoiding post-operative neurological deficits. In order for surgeons to have optimal intraoperative information concerning white matter anatomy, we developed a platform that allows the intra-operative real-time querying of tractography datasets during frameless stereotactic neuronavigation. Structural magnetic resonance imaging (MRI), functional MRI, and diffusion tensor imaging (DTI) were performed on 5 patients before undergoing lesion resection using neuronavigation. During the procedure, the tracked surgical tool tip position was transferred from the navigation system to the 3D Slicer software package, which used this position to seed the white matter tracts around the tool tip location, rendering a geometric visualization of these tracts on the pre-operative images previously loaded onto the navigation system. The clinical feasibility of this approach was evaluated during five cases of lesion resection. In addition, system performance was evaluated by measuring the latency between surgical tool tracking and visualization of the seeded white matter tracts. Lesion resection was performed successfully in all five patients. The seeded white matter 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 fiducial radius size of 4-5mm. Interactive tractography can provide an intuitive way of inspecting critical white matter tracts in the vicinity of the surgical region, allowing the surgeon to have increased intra-operative white matter information to execute the planned surgical resection.

Funding:

• NIH U41 RR019703
• NIH P01 CA67165
• NIH R01 EB006494
• NIH U54 EB005149
• Intelligent Surgical Instruments Project of METI (Japan)
• The Brain Science Foundation and the Klarman Family Foundation

Publication: Int Conf Med Image Comput Comput Assist Interv. 2010;13(Pt 3):383-391. PMID: 20879423 | PDF

Authors: Helen Xu, Andras Lasso, Siddharth Vikal, Peter Guion, Axel Krieger, Aradhana Kaushal, Louis L. Whitcomb, and Gabor Fichtinger

Institutions: Queen's University, Kingston, Canada; National Institutes of Health, Bethesda, USA; Sentinelle Medical Inc., Toronto, Canada; Johns Hopkins University, Baltimore, USA

Background/Purpose: Prostate cancer is a major health threat for men. For over five years, the U.S. National Cancer Institute has performed prostate biopsies with a magnetic resonance imaging (MRI)-guided robotic system. A retrospective evaluation methodology and analysis of the clinical accuracy of this system is reported. Using the pre and post-needle insertion image volumes, a registration algorithm that contains a two-step rigid registration followed by a deformable refinement was developed to capture prostate dislocation during the procedure. 3D Slicer was used to validate the registration algorithm by manually aligning the surfaces of segmented objects in 3D.

Funding:

• NIH R01 CA111288-04
• NIH R01 EB002963-05

Publication: Med Image Comput Comput Assist Interv. 2010;13(Pt 3):457-64. PMID: 20879432 | PDF

Authors: Shamir RR, Tamir I, Dabool E, Joskowicz L, Shoshan Y.

Institution: School of Engineering and Computer Science, The Hebrew University, Jerusalem, Israel.

Background/Purpose: We present a new preoperative planning method for reducing the risk associated with insertion of straight tools in image-guided keyhole neurosurgery. The method quantifies the risks of multiple candidate trajectories and presents them on the outer head surface to assist the neurosurgeon in selecting the safest path. The surgeon can then define and/or revise the trajectory, add a new one using interactive 3D visualization, and obtain a quantitative risk measures. The trajectory risk is evaluated based on the tool placement uncertainty, on the proximity of critical brain structures, and on a predefined table of quantitative geometric risk measures. Our results on five targets show a significant reduction in trajectory risk and a shortening of the preoperative planning time as compared to the current routine method.

Funding:

• FP7 ERC ROBOCAST Grant 21590

Publication: Workshop for Talented Youth

Author: Christopher Wyatt, Ph.D.

Institution: John Hopkins University, Baltimore, MD.

Background/Purpose: This 2010 workshop for the JHU Center for Talented Youth was hosted at Virginia Tech and focused on neuroscience. The event included an interactive session titled "Brain Shape: Using images to predict the development of Alzheimer's Disease." The session included a short introduction to neuroimaging, followed by students, alone or in pairs, using the 3D Slicer software to compare healthy and pathological images of the brain. 100 students ranging in age from 13 to 16 years old attended the event.

Publication: J Vet Med Sci. 2010 Jul;72(7):853-60. PMID: 20179383 | PDF

Authors: Jung MA, Lee MS, Lee IH, Lee AR, Jang DP, Kim YB, Cho ZH, Nahm SS, Eom KD

Institution: Department of Veterinary Radiology and Diagnostic Imaging, College of Veterinary Medicine, Konkuk University.

Background/Purpose: This study was performed to anatomically illustrate the living canine hippocampal formation in three-dimensions (3D), and to evaluate its relationship to surrounding brain structures. Three normal beagle dogs were scanned on a MR scanner with inversion recovery segmented three- dimensoinal gradient echo sequence (known as MP-RAGE: Magnetization Prepared Rapid Gradient Echo). The MRI data was manually segmented and reconstructed into a three-dimensional model using the 3D Slicer software tool. From the three-dimensional model, the spatial relationships between hippocampal formation and surrounding structures were evaluated. With the increased spatial resolution and contrast of the MPRAGE, the canine hippocampal formation was easily depicted. The reconstructed three-dimensional image allows easy understanding of the hippocampal contour and demonstrates the structural relationship of the hippocampal formation to surrounding structures in vivo.

Funding:

• National Research Foundation of Korea Grant funded by the Korean Government. KRF-2008-A003-0061

Publication: J Am Coll Surg. 2010 Jun;210(6):927-33. PMID: 20510801 | PDF

Authors: Tomikawa M, Hong J, Shiotani S, Tokunaga E, Konishi K, Ieiri S, Tanoue K, Akahoshi T, Maehara Y, Hashizume M.

Institution: Department of Future Medicine and Innovative Medical Information, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan.

Background/Purpose: The aim of this study was to report on the early experiences using a real-time 3-dimensional (3D) virtual reality navigation system with open MRI for breast-conserving surgery. STUDY DESIGN: We developed a real-time 3D virtual reality navigation system with open MRI, and evaluated the mismatch between the navigation system and real distance using a 3D phantom. Two patients with nonpalpable MRI-detected breast tumors underwent breast-conserving surgery under the guidance of the navigation system. An initial MRI for the breast tumor using skin-affixed markers was performed immediately before excision. A percutaneous intramammary dye marker was applied to delineate an excision line, and the computer software "3D Slicer" generated a real-time 3D virtual reality model of the tumor and the puncture needle in the breast. Excision of the tumor was performed in the usual manner along the excision line indicated with the dye. The resected specimens were carefully examined histopathologically. RESULTS: The mean mismatch between the navigation system and real distance was 2.01±0.32 mm when evaluated with the 3D phantom. Under guidance by the navigation system, a percutaneous intramammary dye marker was applied without any difficulty. Fiducial registration errors were 3.00 mm for patient no. 1, and 4.07 mm for patient no. 2. Histopathological examinations of the resected specimens of the 2 patients showed noninvasive ductal carcinoma in situ. The surgical margins were free of carcinoma cells. CONCLUSIONS: Real-time 3D virtual reality navigation system with open MRI is feasible for safe and accurate excision of nonpalpable MRI-detected breast tumors. Long-term outcomes of this technique should be evaluated further.

Publication: Annu ORNL Biomed Sci Eng Cent Conf. 2010 May 25;2010:1-4. PMID: 21151892 | PDF

Authors: Covington K, McCreedy ES, Chen M, Carass A, Aucoin N, Landman BA

Institution: Department of Electrical Engineering, Vanderbilt University, Nashville, TN 37215 USA.

Background/Purpose: Clinical research with medical imaging typically involves large-scale data analysis with interdependent software toolsets tied together in a processing workflow. Numerous, complementary platforms are available, but these are not readily compatible in terms of workflows or data formats. Both image scientists and clinical investigators could benefit from using the framework which is a most natural fit to the specific problem at hand, but pragmatic choices often dictate that a compromise platform is used for collaboration. Manual merging of platforms through carefully tuned scripts has been effective, but exceptionally time consuming and is not feasible for large-scale integration efforts. Hence, the benefits of innovation are constrained by platform dependence. Removing this constraint via integration of algorithms from one framework into another is the focus of this work. We propose and demonstrate a light-weight interface system to expose parameters across platforms and provide seamless integration. In this initial effort, we focus on four platforms Medical Image Analysis and Visualization (MIPAV), Java Image Science Toolkit (JIST), command line tools, and 3D Slicer. We explore three case studies: (1) providing a system for MIPAV to expose internal algorithms and utilize these algorithms within JIST, (2) exposing JIST modules through self-documenting command line interface for inclusion in scripting environments, and (3) detecting and using JIST modules in 3D Slicer. We review the challenges and opportunities for light-weight software integration both within development language (e.g., Java in MIPAV and JIST) and across languages (e.g., C/C++ in 3D Slicer and shell in command line tools).

Funding:

• NIH R21 NS064534-01A109
• NIH R21 EB009900

Publication: IEEE Int Conf Robot Autom. 2010 May 3;2010:2068-2073. PMID: 21339851 | PDF

Authors: Majewicz A, Wedlick TR, Reed KB, Okamura AM.

Institution: Department of Mechanical Engineering, Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, MD, USA.

Background/Purpose: Insertion velocity, tip asymmetry, and shaft diameter may influence steerable needle insertion paths in soft tissue. In this paper we examine the effects of these variables on needle paths in ex vivo goat liver, and demonstrate practical applications of robotic needle steering for ablation, biopsy, and brachytherapy. All experiments were performed using a new portable needle steering robot that steers asymmetric-tip needles under fluoroscopic imaging. For bevel-tip needles, we found that larger diameter needles resulted in less curvature, i.e. less steerability, confirming previous experiments in artificial tissue. The needles steered with radii of curvature ranging from 3:4 cm (for the most steerable pre-bent needle) to 2:97m (for the least steerable bevel needle). Pre-bend angle significantly affected needle curvature, but bevel angle did not. We hypothesize that biological tissue characteristics such as inhomogeneity and viscoelasticity significantly increase path variability. These results underscore the need for closed-loop image guidance for needle steering in biological tissues with complex internal structure.

Funding:

• R01 EB006435-03/NIBIB NIH HHS/United States

Publication: Proc. of SPIE Vol. 7624 762421-2 | PDF

Authors: Haiyong Xu, H. Donald Gageb, Pete Santago

Institution: Department of Biomedical Engineering, Wake Forest Univ. Health Sciences, Medical Center Blvd. Winston-Salem, NC, USA.

Background/Purpose: Most colon CAD (computer aided detection) software products, especially commercial products, are designed for use by radiologists in a clinical environment. Therefore, those features that effectively assist radiologists in finding polyps are emphasized in those tools. However, colon CAD researchers, many of whom are engineers or computer scientists, are working with CT studies in which polyps have already been identified using CT Colonography (CTC) and/or optical colonoscopy (OC). Their goal is to utilize that data to design a computer system that will identify all true polyps with no false positive detections. Therefore, they are more concerned with how to reduce false positives and to understand the behavior of the system than how to find polyps. Thus, colon CAD researchers have different requirements for tools not found in current CAD software. We have implemented a module in 3D Slicer to assist these researchers. As with clinicalbcolon CAD implementations, the ability to promptly locate a polyp candidate in a 2D slice image and on a 3D colonbsurface is essential for researchers. Our software provides this capability, and uniquely, for each polyp candidate, thebprediction value from a classifier is shown next to the 3D view of the polyp candidate, as well as its CTC/OC finding. This capability makes it easier to study each false positive detection and identify its causes. We describe features in our colon CAD system that meets researchers’ specific requirements. Our system uses an open source implementation of a 3D Slicer module, and the software is available to the public for use and for extension (http://www2.wfubmc.edu/ctc/download/).

Funding:

• 5R01 CA114492-03

Publication: Neurosurgery. 2010 Apr;66(4):788-95; discussion 795-6. PMID: 20305498 | PDF

Authors: M. Hodaie, J. Quan, D.Q.Chen

Institution: Division of Neurosurgery, University of Toronto and Toronto Western Hospital, Toronto, Canada.

Background/Purpose: Diffusion-based tractography has emerged as a powerful technique for 3-dimensional tract reconstruction and imaging of white matter fibers; however, tractography of the cranial nerves has not been well studied. In particular, the feasibility of tractography of the individual cranial nerves has not been previously assessed. METHODS: 3-Tesla magnetic resonance imaging scans, including anatomic magnetic resonance images and diffusion tensor images, were used for this study. Tractography of the cranial nerves was performed using 3D Slicer software. The reconstructed 3-dimensional tracts were overlaid onto anatomic images for determination of location and course of intracranial fibers. RESULTS: Detailed tractography of the cranial nerves was obtained, although not all cranial nerves were imaged with similar anatomic fidelity. Some tracts were imaged in great detail (cranial nerves II, III, and V). Tractography of the optic apparatus allowed tracing from the optic nerve to the occipital lobe, including Meyer's loop. Trigeminal tractography allowed visualization of the gasserian ganglion as well as postganglionic fibers. Tractography of cranial nerve III shows the course of the fibers through the midbrain. Lower cranial nerves (cranial nerves IX, XI, and XII) could not be imaged well. CONCLUSION: Tractography of the cranial nerves is feasible, although technical improvements are necessary to improve the tract reconstruction of the lower cranial nerves. Detailed assessment of anatomy and the ability of overlaying the tracts onto anatomic magnetic resonance imaging scans is essential, particularly in the posterior fossa, to ensure that the tracts have been reconstructed with anatomic fidelity.

Publication: Master's Thesis, University of Heidelberg February 2010. | PDF

Author: Daniel Hähn

Institution: Medical Informatics, University of Heidelberg, Germany

Background/Purpose: Atherosclerosis of the coronary arteries leads to Coronary Artery Disease (CAD) and is one of the main causes of death worldwide. Diagnosis and investigation of the severity of atherosclerosis is performed through medical imaging. In this context, the central lumen line of coronary arteries is of importance because it can be used for visualization and reconstruction based on reformatted images. We studied algorithms performing vessel enhancement filtering, level set segmentation and centerline computation based on Delaunay tessellation. By composing a pipeline of these, it is possible to extract the centerlines of coronary arteries in Computed Tomography Angiography (CTA) images. We implemented the pipeline as modules in 3D Slicer, an application providing a wide range of tools for medical image processing. This was accomplished by using methods of the Vascular Modeling Toolkit, an open source framework for image-based modeling of blood vessels. We evaluated the pipeline on eight CTA datasets by extracting the centerlines of the right and left coronary arteries. Using a large-scale parameter exploration study, we could achieve an average overlap over 72% of the clinically relevant part of the vessels combined with an average accuracy of 0.47mm by finding individual parameters for each dataset. Through a leave-one-out cross validation approach, we recognized parameter sets targeting the different branches of the arteries suitable for all datasets. Nevertheless, the found pattern lowers the average overlap to 54% and the average accuracy to 0.66mm. The software modules created during this project are available as open source software and suitable for end-users.

Funding: Thomas ­Gessmann Foundation part of the Founder Federation for German Science.

Publication: Med Phys. 2010 Feb;37(2):802-13. PMID: 20229890

Authors: Karnik V.V., Fenster A., Bax J., Cool D.W., Gardi L., Gyacskov I., Romagnoli C., Ward A.D.

Institution: Biomedical Engineering Graduate Program, The University of Western Ontario, London, Ontario N6A 5C1, Canada.

Background/Purpose: Prostate biopsy, performed using two-dimensional (2D) transrectal ultrasound (TRUS) guidance, is the clinical standard for a definitive diagnosis of prostate cancer. Histological analysis of the biopsies can reveal cancerous, noncancerous, or suspicious, possibly precancerous, tissue. During subsequent biopsy sessions, noncancerous regions should be avoided, and suspicious regions should be precisely rebiopsied, requiring accurate needle guidance. It is challenging to precisely guide a needle using 2D TRUS due to the limited anatomic information provided, and a three-dimensional (3D) record of biopsy locations for use in subsequent biopsy procedures cannot be collected. Our tracked, 3D TRUS-guided prostate biopsy system provides additional anatomic context and permits a 3D record of biopsies. However, targets determined based on a previous biopsy procedure must be transformed during the procedure to compensate for intraprocedure prostate shifting due to patient motion and prostate deformation due to transducer probe pressure. Thus, registration is a critically important step required to determine these transformations so that correspondence is maintained between the prebiopsied image and the real-time image. Registration must not only be performed accurately, but also quickly, since correction for prostate motion and deformation must be carried out during the biopsy procedure. The authors evaluated the accuracy, variability, and speed of several surface-based and image-based intrasession 3D-to-3D TRUS image registration techniques, for both rigid and nonrigid cases, to find the required transformations. METHODS: Our surface-based rigid and nonrigid registrations of the prostate were performed using the iterative-closest-point algorithm and a thin-plate spline algorithm, respectively. For image-based rigid registration, the authors used a block matching approach, and for nonrigid registration, the authors define the moving image deformation using a regular, 3D grid of B-spline control points. The authors measured the target registration error (TRE) as the postregistration misalignment of 60 manually marked, corresponding intrinsic fiducials. The authors also measured the fiducial localization error (FLE), the effect of segmentation variability, and the effect of fiducial distance from the transducer probe tip. Lastly, the authors performed 3D principal component analysis (PCA) on the x, y, and z components of the TREs to examine the 95% confidence ellipsoids describing the errors for each registration method. RESULTS: Using surface-based registration, the authors found mean TREs of 2.13±0.80 and 2.09±0.77 mm for rigid and nonrigid techniques, respectively. Using image-based rigid and non-rigid registration, the authors found mean TREs of 1.74±0.84 and 1.50±0.83 mm, respectively. Our FLE was 0.21 mm and did not dominate the overall TRE. However, segmentation variability contributed substantially approximately 50%) to the TRE of the surface-based techniques. PCA showed that the 95% confidence ellipsoid encompassing fiducial distances between the source and target registration images was reduced from 3.05 to 0.14 cm³, and 0.05 cm³ for the surface-based and image-based techniques, respectively. The run times for both registration methods were comparable at less than 60 s. Conclusions: Our results compare favorably with a clinical need for a TRE of less than 2.5 mm, and suggest that image-based registration is superior to surface-based registration for 3D TRUS-guided prostate biopsies, since it does not require segmentation.

Publication: PLoS Pathog 5(9): e1000591. doi:10.1371/journal.ppat.1000591 PMID: 19779568 | PDF

Authors: Adam E. Bennett, Kedar Narayan, Dan Shi, Lisa M. Hartnell, Karine Gousset, Haifeng He, Bradley C. Lowekamp, Terry S. Yoo, Donald Bliss, Eric O. Freed, Sriram Subramaniam

Institution: Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA.

Background/Purpose: HIV-1-containing internal compartments are readily detected in images of thin sections from infected cells using conventional transmission electron microscopy, but the origin, connectivity, and 3D distribution of these compartments has remained controversial. Here, we report the 3D distribution of viruses in HIV-1-infected primary human macrophages using cryo-electron tomography and ion-abrasion scanning electron microscopy (IA-SEM), a recently developed approach for nanoscale 3D imaging of whole cells. Using IA-SEM, we show the presence of an extensive network of HIV-1-containing tubular compartments in infected macrophages, with diameters of 150–200 nm, and lengths of up to 5 mm that extend to the cell surface from vesicular compartments that contain assembling HIV-1 virions. These types of surface-connected tubular compartments are not observed in T cells infected with the 29/31 KE Gag-matrix mutant where the virus is targeted to multi-vesicular bodies and released into the extracellular medium. IA-SEM imaging also allows visualization of large sheet-like structures that extend outward from the surfaces of macrophages, which may bend and fold back to allow continual creation of viral compartments and virion-lined channels. This potential mechanism for efficient virus trafficking between the cell surface and interior may represent a subversion of pre-existing vesicular machinery for antigen capture, processing, sequestration, and presentation.

Publication: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. PMID: 20033581 | PDF

Authors: R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler

Institution: Department of Oral and Maxillofacial Surgery, Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium.

Background/Purpose: Our knowledge of facial muscles is based primarily on atlases and cadaveric studies. This study describes a non-invasive in vivo method (3D MRI) for segmenting and reconstructing facial muscles in a three-dimensional fashion. METHODS: Three-dimensional (3D), T1-weighted, 3 Tesla, isotropic MRI was applied to a subject. One observer performed semi-automatic segmentation using the Editor module from the 3D Slicer software (Harvard Medical School, Boston, MA, USA), version 3.2. RESULTS: We were able to successfully outline and three-dimensionally reconstruct the following facial muscles: pars labialis orbicularis oris, m. levatro labii superioris alaeque nasi, m. levator labii superioris, m. zygomaticus major and minor, m. depressor anguli oris, m. depressor labii inferioris, m. mentalis, m. buccinator, and m. orbicularis oculi. CONCLUSIONS: 3D reconstruction of the lip muscles should be taken into consideration in order to improve the accuracy and individualization of existing 3D facial soft tissue models. More studies are needed to further develop efficient methods for segmentation in this field.

Author: Caitlin Berrigan

Assistance: Marianna Jakab, BWH

Special Thanks: J. Levi Schmidt (MIT), Tom Lutz (MIT Media Lab), Neil Gershenfeld (MIT Center for Bits & Atoms), Clare Tempany (BWH)

Institution: MIT Visual Arts Program

Background/Purpose: Traces is a renewable sculpture of the artist’s own disembodied kidney, cast in frozen spit. Every two hours a new frozen organ is put on display, only to melt and drip away. The artist - using 3D Slicer - carefully traced the topography of her internal organ from a 3D MRI, consisting of hundreds of sequential medical images, in order to materialize its form outside of her body. Traces is a poetic deterritorialization of medical biotechnologies, organs without bodies and fleshy displacements. It calls attention to the alienability of body parts and the vast global industry that sustains the promise of an infinitely repairable body.

Funding:

• MIT Council for the Arts

Institution: Multiple Sclerosis Center

Background/Purpose: The CLIMB study is a longitudinal natural history study conducted at the Partners Multiple Sclerosis Center. All patients enrolled in the CLIMB undergo a detailed neurological examination at least annually, and have a brain MRI and a blood draw with associated immunological analysis on an annual basis. Within the CLIMB study, the following cohorts of patients are enrolled: relapsing-remitting MS (RRMS) and secondary progressive MS (SPMS), as well as patients with primary progressive MS (PPMS), CIS, and benign MS.

Over 30 publications have been generated from CLIMB-related data since its inception. The MRI Analysis Center of the Partners MS Center manages routine MRI processing of all CLIMB study subject MRIs. Routine processing includes calculation of T2 lesion volume and brain parenchymal fraction and number of gadolinium enhancing lesions. Image Workflow system based on Standart Operationg Procedures/Modules in Database system to allow for query from data fields as well as in image space. Several advanced image visualization packages are used for visualization and analysis. These include SLICER (www.slicer.org), OSIRIX (www.osirix-viewer.com) and GDC (in house). Slicer and OSIRIX are open source packages, for which CNI had developed plugins and scripts to streamline workflow.

Following processing steps are performed using Slicer software:

• Quality Assurance of Grayscale original MRI images by experts to qualify images set for further analysis (accept or reject)
• Manual Correction of the ICC (intracranial cavity) of the dataset for further Segmentation;
• Quality assurance of segmented label maps based on visual expertise of segmented label map and if required the manual correction of segmented label maps

Principal Investigator: Rohit Bakshi

Institution: Laboratory for Neuroimaging Research, Partners MS Center

Background/Purpose: We used quantitative MRI parameters such as T2 lesion volume (T2LV) and brain parenchymal fraction (BPF) to assess treatment in patients with MS. T2 lesion volume and BPF were measured using template-driven segmentation (TDS+) algorithm by automated pipeline. Medical image data were visualized by 3DSlicer to provide QC for original data, segmented output and perform manual correction on required steps of processing pipeline.

Funding:

• Biogen

Principal Investigator: Marilyn S. Albert

Institution: Johns Hopkins Alzheimer’s Disease Research Center

Background/Purpose: The goal of this project was the utilization of magnetic resonance imaging for morphometric analysis and tissue characterization to distinguish the patterns of brain atrophy and gray or white matter changes and white matter signal abnormalities in normal aging or Alzheimer's disease.

Image analysis comprised an automated tissue segmentation into the intracranial cavity (ICC) and subclasses of white matter (WM), gray matter (GM), cerebrospinal fluid (CSF), and WM signal abnormalities (WMSA). Brain parenchymal fraction (BPF) was defined as BPF=(1-CSF)/ICC. Medical image data were visualized by Slicer to provide QC for original grayscale data, segmented output and perform manual correction of ICC.

Funding:

• NIH/NIA Grant P01 AG04953-18

Principal Investigator: Lewis A. Lipsitz

Institution: Institute for Aging Research (IFAR)

Background/Purpose: The project focuses on abnormal blood pressure regulation and its relationship to the development of falls and syncope in the elderly.

Slicer was used to provide visualization during QC step of original data (1.5T &3T), segmented output and perform manual correction on required steps of processing pipeline as well as corpus callosum outline for parcellation.

Principal Investigator: Tanuja Chitnis

Institution: Partners Pediatric MS Center

Background/Purpose: We used quantitative MRI parameters such as T2 lesion volume (T2LV) to assess treatment in patients with POMS. The T2-lesion volume of the brain was manually outlined using 3D Slicer (www.slicer.org).

Funding: Pediatric Multiple Sclerosis Centers of Excellence Grant from the National Multiple Sclerosis Society

Principal Investigator: Tanuja Chitnis

Institution: Partners Pediatric MS Center

Background/Purpose: To assess differences in MRI-derived lesion volume and brain parenchymal fraction (BPF) between patients with pediatric- and adult-onset Multiple Sclerosis (MS).

T2 lesion volume and BPF were measured using template-driven segmentation (TDS+) algorithm by automated pipeline of the Multiple Sclerosis Database Project. Medical image data were visualized by Slicer to provide QC for original data, segmented output and perform manual correction on required steps of processing pipeline.

Funding: Pediatric Multiple Sclerosis Centers of Excellence Grant from the National Multiple Sclerosis Society

Principal Investigator: Tanuja Chitnis

Institution: Partners Pediatric MS Center

Background/Purpose: The goal of this project is to assess the characteristics of the pediatric MS patient population and increase education and awareness of this disease subtype.

Slicer is used to QC MRI images coming to the multi-center MRI data repository at the Center for Neurological Imaging (CNI) at Brigham and Women’s Hospital.

Funding: Pediatric Multiple Sclerosis Centers of Excellence Grant from the National Multiple Sclerosis Society

Institution: Multiple Sclerosis Center

Background/Purpose: Project is an initiative to design, develop and implement a database system integrating all aspects of clinical data with medical image data. This image-centric database will enable users to visualize clinical data, including laboratory results, immunologic data, and examination scores, simultaneously with that individual’s MRI images. By integrating the medical images and clinical patient data in a comprehensive system, the efficiency of patient care and data analysis is dramatically improved. This database is another small step towards our ultimate goal: Finding a cure for MS.

Image Workflow system based on Standart Operationg Procedures/Modules in Database system to allow the day-to-day management and query from data fields to ensure that trial was performed according to SOPs by managing the efforts of MRI research personnel, quality control of data, image analysis and image processing as a part of quantitative pipeline for trial. Slicer (www.slicer.org) advanced image visualization package is used for visualization and analysis MRI data to provide T2 lesion volume and BPF volumetric measurements.

Publication: TBA

Authors: Ganesh Thiagarajan, Mark Johnson, Mark Dallas, Yunkai Lu

Institution: University of Missouri-Kansas City

Background/Purpose: It has been hypothesized that osteocytes are stimulated by local strain distribution within the bone subjected to mechanical loadings. In this research project, the mouse forearm model was built which was later used for extensive finite element study. The study will be the first in the field to include the radius in the numerical analysis to examine its effect on the load distribution between the ulna/radius. In order to preserve the geometrical details of the bones, the cavities were traced independently. Then a 3D volume subtraction was performed in another software to produce the exact CAD model of the bone structure. The results of the current research are expected to shed light on how bone perceives mechanical load and the pathway whereby the physical load is transduced into a biochemical event and eventually results in new bone formation. The study will help in developing new treatments for bone diseases such as osteoporosis.

Funding:

• Missouri Life Science Research Board
• UMKC Center of Excellence in Mineralized Tissues

Publication: Neurobiol Aging. 2009 May 8. PMID: 19428145 | PDF

Authors: Moscufo N, Guttmann C, Meier D, Csapo I, Hildenbrand P, Healy B, Schmidt J, Wolfson L

Institution: Center for Neurological Imaging, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

Background/Purpose: This study investigated the relationship of brain white matter (WM) lesions affecting specific neural networks with decreased mobility in ninety-nine healthy community-dwelling subjects ≥75 years old prospectively enrolled by age and mobility status. We assessed lesion burden in the genu, body and splenium of corpus callosum; anterior, superior and posterior corona radiata; anterior and posterior limbs of internal capsule; corticospinal tract; and superior longitudinal fasciculus. Burden in the splenium of corpus callosum (SCC) demonstrated the highest correlation particularly with walking speed (r=0.4, p<10^-4), and in logistic regression it was the best regional predictor of low mobility performance. We also found that independent of mobility, corona radiata has the largest lesion burden with anterior (ACR) and posterior (PCR) aspects being the most frequently affected. The results suggest that compromised inter-hemispheric integration of visuospatial information through the SCC plays an important role in mobility impairment in the elderly. The relatively high lesion susceptibility of ACR and PCR in all subjects may obscure the importance of these lesions in mobility impairment. 3D Slicer application has been used in all the imaging analysis steps, which included intracranial cavity outline, one- and two-channel brain tissue segmentation, labelmap outputs expert review and manual correction, image comparison, volume determination, and three-dimensional modeling.

Funding:

• NIH 5 P41 RR13218
• National Institute on Aging AG022092
• National Institute on Aging Training Grant AG022092-01A1S1
• University of Connecticut Health Center General Clinical Research Center Grant M01 RR06192

Publication: Student Research Project 2009 Apr; | PDF

Author: Daniel Hähn

Institution: Medical Informatics, University of Heidelberg

Background/Purpose: The extraction of vessels in two- and three-dimensional images is part of many clinical analysis tasks. Surgical and radiology procedures often involve the visualization and quantification of vessels in order to perform surgical planning or diagnostics. There is no single segmentation method that can extract vessels from every medical image modality, but different approaches and robust algorithms exist. Various published key algorithms are available within an open-source framework for image-based modeling of blood vessels, referred to as the Vascular Modeling Toolkit (VMTK). The library of VMTK was made available in 3D Slicer, an application providing a wide range of tools for medical image processing. This was realized using a hidden loadable module approach in order to provide a flexible way of distributing and including the library. To evaluate and verify the integration, a software module offering VMTK level set segmentation methods within 3D Slicer was created. With the successful connection of the two above mentioned software solutions, processing pipelines between VMTK code and other algorithms can be established. Several techniques for three dimensional reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels are now accessible to the 3D Slicer developer. The reference implementation for accessing VMTK, as well as the created library module are available as open-source software.

Funding:

• Thomas ­Gessmann Foundation part of the Founder Federation for German Science

Publication: PLoS ONE. 2009; 4(4): e5265. PMID: 19370155 | PDF

Authors: Nicolas Cherbuin¹, Kaarin J. Anstey¹, Chantal Réglade-Meslin¹, and Perminder S. Sachdev^2,3

Institution: ¹Centre for Mental Health Research, Australian National University, Canberra, Australian Capital Territory, Australia.

²School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia.

³Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, New South Wales, Australia.

Background/Purpose: Each segmented volume was inspected by producing a 3D model using the Slicer software package (www.slicer.org) and its quality rated: a) no or minor defects (estimated to be smaller than ,0.5% of total volume) b) moderate defects (,0.5–5% of total volume), major defects (greater than 5% of total volume). Exemplars are given in Figure 1.

Funding:

• NHMRC of Australia Unit Grant No. 973302, Program Grant No. 179805
• NHMRC project grant No. 157125
• Australian Rotary Health Research Fund
• National Super-computer facility APAC
• Australian Brewers Foundation
• NHMRC grant No. 418020
• NHMRC Research Fellowship No. 366756.

Publication: The International Journal of Virtual Reality, 2009, 8(1): 9-16. | PDF

Authors: Huy Hoang Tran, Kiyoshi Matsumiya, Ken Masamune, Ichiro Sakuma, Takeyoshi Dohi and Hongen Liao

Institution: Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan.

Background/Purpose: In this paper, we mainly focus on a high-speed IV rendering method that allows interactions to be done in almost real-time, while maintaining the rendered result at an acceptable quality. We also built a navigation system based on the open source software 3D Slicer so that many tasks can be done in a single application.

Funding:

• Ministry of Education, Culture, Sports, Science and Technology (MEXT)
• Grant for Industrial Technology Research (07C46050) of New Energy and Industrial Technology Development Organization
• Communications R & D Promotion Programme (062103006) of the Ministry of Internal Affairs and Communications

Publication: Psychiatry and Clinical Neurosciences 2009; 63: 266-276. PMID: 19566756 | PDF

Authors: Hayano F, Nakamura M, Asami T, Uehara K, Yoshida T, Roppongi T, Otsuka T, Inoue T, Hirayasu Y

Institution: Department of Psychiatry, Yokohama City University, Yokohama, Kanagawa, Japan.

Background/Purpose: Anxiety a core feature of panic disorder, is linked to function of the amygdala. Volume alterations in the brain of patients with panic disorder have previously been reported, but there has been no report of amygdala volume association with anxiety. METHODS: Volumes of hippocampus and amygdala were manually measured using magnetic resonance imaging obtained from 27 patients with panic disorder and 30 healthy comparison subjects. In addition the amygdala was focused on, applying small volume correction to optimized voxel-based morphometry (VBM). State-Trait Anxiety Inventory and the NEO Personality Inventory Revised were also used to evaluate anxiety. RESULTS: Amygdala volumes in both hemispheres were significantly smaller in patients with panic disorder compared with control subjects (left: t = -2.248, d.f. = 55, P = 0.029; right: t = -2.892, d.f. = 55, P = 0.005). VBM showed that structural alteration in the panic disorder group occurred on the corticomedial nuclear group within the right amygdala (coordinates [x,y,z (mm)]: [26,-6,-16], Z score = 3.92, family-wise error-corrected P = 0.002). The state anxiety was negatively correlated with the left amygdala volume in patients with panic disorder (r = -0.545, P = 0.016). CONCLUSIONS: These findings suggested that the smaller volume of the amygdala may be associated with anxiety in panic disorder. Of note, the smaller subregion in the amygdala estimated on VBM could correspond to the corticomedial nuclear group including the central nucleus, which may play a crucial role in panic attack.

Funding:

• Ministry of Health, Labor and Welfare of Japan

Publication: Int Conf Med Image Comput Comput Assist Interv. 2009;12(Pt 1): 1–8. PMID: 20425964 | PDF.

Authors: Jagadeesan Jayender, Rajni V. Patel, Gregory F. Michaud, Nobuhiko Hata

Institution: Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA and The University of Western Ontario, Canadian Surgical Technologies and Advanced Robotics (CSTAR), London, ON, Canada.

Background/Purpose: The preferred method of treatment for Atrial Fibrillation (AF) is by catheter ablation wherein a catheter is guided into the left atrium through a transseptal puncture. However, the transseptal puncture constrains the catheter, thereby limiting its maneuverability and increasing the difficulty in reaching various locations in the left atrium. In this project, we have developed a computational algorithm to choose the optimal transseptal puncture location to obtain maximum maneuverability of the catheter for performing cardiac ablation. We have employed an optimization algorithm to maximize the Global Isotropy Index (GII) to evaluate the optimal transseptal puncture location. Preoperative MR/CT images of the heart are segmented using the open source image-guided therapy software, 3D Slicer, to obtain models of the left atrium and septal wall. These models are input to the optimization algorithm to evaluate the optimal transseptal puncture location. The results of the GII algorithm are color-mapped on the model of the septal wall and displayed to the user in Slicer.

Funding:

• Intelligent Surgical Instruments Project of METI, Japan.

Resource Support: NIH National Center for Image Guided Therapy U41 RR019703, NIH National Alliance for Medical Image Computing U54 EB005149

Publication: Neurobiol Aging. 2009. PMID: 19570593 | PDF

Authors: Kristine B. Walhovd, Lars T. Westlye, Inge Amlien, Thomas Espeseth, Ivar Reinvang, Naftali Raz, Ingrid Agartz, David H. Salat, Doug N. Greve, Bruce Fischl, Anders M. Dale, Anders M. Fjell

Institution: Center for the Study of Human Cognition, Department of Psychology, University of Oslo, Norway.

Background/Purpose: Magnetic resonance imaging (MRI) is the principal method for studying structural age-related brain changes in vivo. However, previous research has yielded inconsistent results, precluding understanding of structural changes of the ageing brain. This inconsistency is due to methodological differences and/or different aging patterns across samples. To overcome these problems, we tested age effects on 17 different neuroanatomical structures and total brain volume across five samples, of which one was split to further investigate consistency (883 participants). Widespread age-related volume differences were seen consistently across samples. In four of the five samples, all structures, except the brainstem, showed age-related volume differences. The strongest and most consistent effects were found for cerebral cortex, pallidum, putamen and accumbens volume. Total brain volume, cerebral white matter, caudate, hippocampus and the ventricles consistently showed non-linear age functions. Healthy aging appears associated with more widespread and consistent age-related neuroanatomical volume differences than previously believed.

Funding:

• The Norwegian Research Council
• NIH R01 NS39581, R01 RR16594, P41 RR14075, R01 AG11230, R01 RR13609)
• The Mental Illness and Neuroscience Discovery (MIND) Institute
• The Biomedical Informatics Research Network Project (BIRN, http://www.nbirn.net, funded by the National Center for Research Resources at the National Institutes of Health (NCRR BIRN Morphometric Project BIRN002))
• The Wallenberg Foundation and the Swedish Medical Research Council (K2004-21X-15078-01A 45, K2007-62X-15077-04-1, and K2007-62X-15078-04-3)
• Eastern Norway Health Authority (A135).

Publication: Neuroimage. 2009 Mar 1;45(1):215-23. PMID: 19056499 | PDF

Authors: K.B. Walhovd, A.M. Fjell, I. Amlien, R. Grambaite, V. Stenset, A. Bjørnerud, I. Reinvang, L. Gjerstad, T. Cappelen, P. Due-Tønnessen, T. Fladby

Institution: Center for the Study of Human Cognition, Department of Psychology, University of Oslo, Norway.

Background/Purpose: This study compared sensitivity of FDG-PET, MR morphometry, and diffusion tensor imaging (DTI) derived fractional anisotropy (FA) measures to diagnosis and memory function in mild cognitive impairment (MCI). Patients (n = 44) and normal controls (NC, n = 22) underwent FDG-PET and MRI scanning yielding measures of metabolism, morphometry and FA in nine temporal and parietal areas affected by Alzheimer's disease and involved in the episodic memory network. Patients also underwent memory testing (RAVLT). Logistic regression analysis yielded 100% diagnostic accuracy when all methods and ROIs were combined, but none of the variables then served as unique predictors. Within separate ROIs, diagnostic accuracy for the methods combined ranged from 65.6% (parahippocampal gyrus) to 73.4 (inferior parietal cortex). Morphometry predicted diagnostic group for most ROIs. PET and FA did not uniquely predict group, but a trend was seen for the precuneus metabolism. For the MCI group, stepwise regression analyses predicting memory scores were performed with the same methods and ROIs. Hippocampal volume and FA of the retrosplenial WM predicted learning, and hippocampal metabolism and parahippocampal cortical thickness predicted 5 minute recall. No variable predicted 30 minute recall independently of learning. In conclusion, higher diagnostic accuracy was achieved when multiple methods and ROIs were combined, but morphometry showed superior diagnostic sensitivity. Metabolism, morphometry and FA all uniquely explained memory performance, making a multi- modal approach superior. Memory variation in MCI is likely related to conversion risk, and the results indicate potential for improved predictive power by the use of multimodal imaging.

Funding:

• Norwegian Research Concil.

Publication: Cereb Cortex. 2009 Mar;19(3):554-62. PMID: 18552356 | PDF

Authors: Lewis JD, Theilmann RJ, Sereno MI, Townsend J.

Institution: Department of Cognitive Science, University of California-San Diego, La Jolla, CA, USA.

Background/Purpose: Using diffusion tensor imaging and tractography to detail the patterns of interhemispheric connectivity and to determine the length of the connections, and formulae based on histological results to estimate degree of connectivity, we show that connection length is negatively correlated with degree of connectivity in the normal adult brain. The degree of interhemispheric connectivity--the ratio of interhemispheric connections to total corticocortical projection neurons--was estimated for each of 5 subregions of the corpus callosum in 22 normal males between 20 and 45 years of age (mean 31.68; standard deviation 8.75), and the average length of the longest tracts passing through each point of each subregion was calculated. Regression analyses were used to assess the relation between connection length and the degree of connectivity. Connection length was negatively correlated with degree of connectivity in all 5 subregions, and the regression was significant in 4 of the 5, with an average r(2) of 0.255. This is contrasted with previous analyses of the relation between brain size and connectivity, and connection length is shown to be a superior predictor. The results support the hypothesis that cortical networks are optimized to reduce conduction delays and cellular costs.

Funding:

• R01 AG18030/AG/NIA NIH HHS/United States

Authors: Reuben R Shamir, Leo Joskowicz, Giancarlo Ferrigno

Institution: School of Engineering and Computer Science, The Hebrew University of Jerusalem, Israel.

Background/Purpose: The goal of the European FP7 ROBOCAST project is to develop a system for keyhole neurosurgery. ROBOCAST integrates optical and electromagnetic localization devices with two modified commercial surgical robots: 1. PathFinder (Prosurgics Ltd, UK), which is used for gross positioning, and; 2. MARS (Mazor Surgical Technologies Ltd, Israel), which is used for fine positioning. A third snake-like robot, currently under development, will be attached to the MARS robot and is intended for curved paths. The system includes as well a haptic device, a tracked ultrasound probe and a micro Doppler ultrasound probe. This sensor and actuation redundancy is expected to yield higher accuracy and robustness, to significantly increase the patient safety, and to allow new procedures. The ROBOCAST software is based on Slicer 3.4 and uses many of its functions.

Funding:

• FP7 European project number ICT-2007-215190-ROBOCAST.

Authors: Reuben R. Shamir, Ran Roth, Leo Joskowicz, Luca Antiga, Roberto I. Foroni, Yigal Shoshan

Institution: School of Engineering and Computer Science, The Hebrew University of Jerusalem, Israel.

Background/Purpose: We present a new preoperative planning method to better assess and reduce the risk caused by a misplacement of surgical tools in image-guided keyhole neurosurgery. The goal is to quantify the risk of a proposed straight trajectory and to find the trajectory with the lowest risk to hit nearby brain structures based on pre-operative CT/MRI images and their segmentation. First, distance maps are computed on the segmented data such that each voxel on the preoperative CT/MRI image is associated with a vector of distances to each of the segmented structures. A risk volume is then created from the distance maps such that a risk ratio is computed based on the vector of distances associated with each voxel. Next, the risk for each possible trajectory is computed such that the risk along a trajectory is assigned with the maximal risk ratio of intersected voxels. The trajectory that is associated with the lowest risk is presented using Slicer 3.2 to the neurosurgeon for further revision. The neurosurgeon can revise the suggested trajectory and can add new paths using interactive 3D visualization and quantitative risk assessment. The interactive 3D visualization shows the segmented structures to be avoided along with a geometric structure that envelopes the defined trajectory and represents the localization uncertainty. In addition, candidate entry points are represented by the outer head surface that is extracted automatically from the patient’s preoperative image and the neurosurgeon can select parts of the surface to restrict the optional entry points. A table, called ‘risk card’, of quantitative measures regarding the risk that is associated with the defined trajectory is presented. It shows the neurosurgeon meaningful geometrical information, including the path length and distance of segmented structures to the path. For the initial validation, we have compared the conventional approach for trajectory planning with our method on 8 targets selected at various locations on a clinical Magnetic Resonance Angiography (MRA) head image. For each target, the user selected two trajectories: one with the conventional method based on the axial, sagittal, and coronal 2D views of the original MRA image, and the second with our method. Our preliminary results show a significant reduction in trajectory risk and planning time when compared to the conventional method.

Funding:

• FP7 European project number ICT-2007-215190-ROBOCAST.

Publication: Can J Vet Res. 2009 Jul;73(3):205-11. PMID: 19794893 | PDF.

Authors: Jonathan E. Phillips, Lunan Ji, Maria A. Rivelli, Richard W. Chapman, Michel R. Corboz.

Institution: Pulmonary and Peripheral Neurobiology, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA.

Background/Purpose: Continuous isometric microfocal X-ray computed tomography (CT) scans were acquired from an AKR/J mouse, Brown-Norway rat, and Hartley guinea pig. The anatomy and volume of the paranasal sinus cavities were defined from 2-dimensional (2-D) and 3-dimensional (3-D) CT images. Realistic 3-D images were reconstructed and used to determine the anterior maxillary, posterior maxillary, and ethmoid sinus cavity airspace volumes (mouse: 0.6, 0.7, and 0.7 mm 3, rat: 8.6, 7.7, and 7.0 mm3, guinea pig: 63.5, 46.6 mm3, and no ethmoid cavity, respectively). The mouse paranasal sinus cavities are similar to the corresponding rat cavities, with a reduction in size, while the corresponding maxillary sinus cavities in the guinea pig are different in size, location, and architecture. Also, the ethmoid sinus cavity is connected by a common drainage pathway to the posterior maxillary sinus in mouse and rat while a similar ethmoid sinus was not present in the guinea pig. We conclude that paranasal sinus cavity airspace opacity (2-D) or volume (3-D) determined by micro-CT scanning may be used to conduct longitudinal studies on the patency of the maxillary sinus cavities of rodents. This represents a potentially useful endpoint for developing and testing drugs in a small animal model of sinusitis.

Funding:

• Schering-Plough Research Institute, Kenilworth, New Jersey, USA.

Publication: Poster Presentation at the Second International Workshop on Pulmonary Image Analysis. | Poster, Paper. Oral Presentation at Advanced Concepts for Intelligent Vision Systems, ACIVS 2009.

Authors: Carlos S. Mendoza, Begoña Acha, Carmen Serrano.

Institution: University of Sevilla, Signal Processing Department.

Background/Purpose: We have developed a general segmentation framework based on a contrast-based self-assessed region growing strategy. Thanks to a previous normalization stage, a wide variety of CT imaging conditions are supported, requiring limited user intervention. Although multiple seeds are accepted for performance boosting, only a single-seed selection stage is required for most of our application specific tissues. The detection of the optimal parameters is managed internally using a measure of the varying contrast of the growing region. Validation is provided for some synthetic images, and also for real CT images. Results have been obtained in the context of surgical planning (bone, muscle and fat segmentation) and pulmonary image analysis (airway segmentation).

Funding:

• "Fundación Reina Mercedes" from "Hospital Universitario Virgen del Rocío" (Seville, Spain)
• "Consejería de Salud de la Junta de Andalucía".
• Carlos S. Mendoza was supported by a doctoral scholarship financed by University of Seville, Spain.

Publication: Insight Journal, Sep 15, 2009. [1]

Authors: Nicolas Rannou¹, Sylvain Jaume², Steve Pieper³, Ron Kikinis³

Institution: ¹ISEN Brest (France), ²MIT CSAIL, ³Harvard Medical School BWH

Background/Purpose: Many neuroanatomy studies rely on brain tissue segmentation in Magnetic Resonance images (MRI). The Expectation-Maximization (EM) theory offers a popular framework for this task. We studied the EM algorithm developed at the Surgical Planning Laboratory (SPL) at Harvard Medical School and implemented in the Slicer3 software. We observed that the segmentation lacks accuracy if the image exhibits some intensity inhomogeneity. Moreover the optimum parameters are challenging to estimate. This document aims at describing our solutions within the context of statistical modeling. Our contributions range from algorithm improvements to novel representations of the statistical distribution model. First we added a bias field correction module and exposed the most significant parameters. Second we proposed a new way to select the distribution of the tissues to be segmented. Finally we designed a set of interactive tools to make the segmentation process easier and more accurate. To validate the new segmentation pipeline, we performed our experiments on MRI data and a clinical expert evaluated our results.

Publication: Poster Presentation at the 80th Conference of the German ENT Society. | PDF.

Authors: A. L. Nagy, A. Tanács, A. Czesznak, Gy. Smehák, F. Tóth, L. Rovó, J. Jóri, J. G. Kiss

Institution: University of Szeged, Department of Oto-rhino-laryngology and Head, Neck Surgery

Background/Purpose: Most of the CT and MR data is stored nowadays on digital media. This opens up new possibilities for us to inspect these data. In our department we evaluated the use of the 3D Slicer software, which is free, open source and is being actively developed. In oto-rhino-laryngology we often encounter situations where the exact localization and estimation of the size of a lesion, or tumor is of critical importance. Especially in the neck and the facial region an extended resection may easily cause damage to the function of the affected organ. The preservation of the swallowing function in case of the neck, and the preservation of sight in interventions around the orbita are two of these areas. By visualizing these space-occupying lesions we were able to plan and carry out the surgery more precisely.

Publication: ECR Today 2009 March 9/10:23. | PDF.

Institution: Medical University of Vienna, Austria.

Authors: T. Dobrocky, H. Kubiena, R. Kikinis, J. Kettenbach

Background/Purpose: Slow-flow vascular malformations, such as venous and lymphatic lesions, are most often recognised in infancy and are thus characterised by a rapid expansion. The majority of these lesions are found in the head and neck region, where many options for treatment modalities (drug therapy, percutaneous sclerotherapy, surgical resection) have been reported in the literature. In many cases, excellent results have been achieved by ultrasound-guided or fluoroscopy-guided percutaneous sclerotherapy, sometimes combined with final surgical resection (see figure). Diagnostic MRI of vascular malformations allows non-invasive treatment planning and follow-up, with excellent soft-tissue contrast.

Publication: Otolaryngol Head Neck Surg. 2009 Jan;140(1):96-102. PMID: 19130970 | PDF

Authors: Matsumoto N, Hong J, Hashizume M, Komune S.

Institution: Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Background/Purpose: A new, minimally invasive registration method was developed for image-guided otologic surgery. We utilized laser-sintered template of the patient's bone surface to transfer the virtual markers to the patient's bone intraoperatively and eliminated the necessity for preoperative marker positioning or additional CT scan. STUDY DESIGN: Simulation surgeries and clinical application. SUBJECTS AND METHODS: We measured registration errors in 10 trials using replicas and six ear surgeries (two cochlear implant insertions, four translabyrinthine acoustic tumor removals). RESULTS: The target registration errors varied among the surgical targets. Errors were less than 1 mm near the cochlear implant insertion target both in phantom study and in actual surgeries. CONCLUSION: Our newly developed method reduced the preoperative procedures for patients but did not reduce the accuracy in cochlear implant surgery. Our method would be a useful image-guided surgery method in the field of otology, where both accuracy and noninvasiveness are required.

Funding:

• Grant-in-Aid for Young Scientists (A) No. 20689031 from Japan Society for the Promotion of Science (JSPS)

Publication: Neuroimage. 2008 Oct 1;42(4):1654-68. PMID: 18620064 | PDF

Authors: Anders M. Fjell, Lars T. Westlye, Doug N. Greve, Bruce Fischl, Thomas Benner, André J.W. van der Kouwe, David Salat, Atle Bjørnerud, Paulina Due-Tønnessen, Kristine B. Walhovd

Institution: Center for the Study of Human Cognition, Department of Psychology, University of Oslo, Norway.

Background/Purpose:There is still limited knowledge about the relationship between different structural brain parameters, despite huge progress in analysis of neuroimaging data. The aim of the present study was to test the relationship between fractional anisotropy (FA) from diffusion tensor imaging (DTI) and regional white matter (WM) volume. As WM volume has been shown to develop until middle age, the focus was on changes in WM properties in the age range of 40 to 60 years. 100 participants were scanned with magnetic resonance imaging (MRI). Each hemisphere was parcellated into 35 WM regions, and volume, FA, axial, and radial diffusion in each region were calculated. The relationships between age and the regional measures of FA and WM volume were tested, and then FA and WM volume were correlated, corrected for intracranial volume, age, and sex. WM volume was weakly related to age, while FA correlated negatively with age in 26 of 70 regions, caused by a mix of reduced axial and increased radial diffusion with age. 23 relationships between FA and WM volume were found, with seven being positive and sixteen negative. The positive correlations were mainly caused by increased radial diffusion. It is concluded that FA is more sensitive than volume to changes in WM integrity during middle age, and that FA-age correlations probably are related to reduced amount of myelin with increasing age. Further, FA and WM volume are moderately to weakly related and to a large extent sensitive to different characteristics of WM integrity.

Funding:

• P41 RR14075 (RR) funded by NCRR NIH HHS
• R01 EB001550 (EB) funded by NIBIB NIH HHS
• R01 NS39581 (NS) funded by NINDS NIH HHS
• R01 RR13609 (RR) funded by NCRR NIH HHS
• R01 RR16594 (RR) funded by NCRR NIH HHS
• R01 EB006758 (EB) funded by NIBIB NIH HHS
• R01 NS052585-01 (NS) funded by NINDS NIH HHS
• U24 RR021382 (RR) funded by NCRR NIH HHS

Publication: Psychiatry Clin Neurosci. 2008 Jun;62(3):322-30. PMID: 18588593 | PDF

Authors: Asami T, Hayano F, Nakamura M, Yamasue H, Uehara K, Otsuka T, Roppongi T, Nihashi N, Inoue T, Hirayasu Y.

Institution: Department of Psychiatry, Yokohama City University School of Medicine, Yokohama, Japan.

Background/Purpose: Recent neuroimaging studies have suggested that the anterior cingulate cortex (ACC) has an important role in the pathology of panic disorder. Despite numerous functional neuroimaging studies that have elucidated the strong relationship between functional abnormalities of the ACC and panic disorder and its symptoms and response to emotional tasks associated with panic disorder, there has been no study showing volumetric changes of the ACC or its subregions. METHODS: To clarify the structural abnormalities of ACC and its subregions, the combination of region of interest (ROI) and optimized voxel-based morphometry (VBM) methods were performed on 26 patients with panic disorder, and 26 age and sex-matched healthy subjects. In the ROI study, ACC was divided into four subregions: dorsal, rostral, subcallosal and subgenual ACC. RESULTS: The results of the manually traced ROI volume comparison showed significant volume reduction in the right dorsal ACC. VBM also showed a volume reduction in the right dorsal as well as a part of the rostral ACC as a compound mass. CONCLUSIONS: Both manual ROI tracing and optimized VBM suggest a subregion-specific pattern of ACC volume deficit in panic disorder. In addition to functional abnormalities, these results suggest that structural abnormalities of the ACC contribute to the pathophysiology of panic disorder.

Funding:

• Grant-in-Aid for Scientific Research (No. 14370294) from the Ministry of Education, Science, Sports and Culture, Japan.

Publication: Heart Rhythm. 2008 Apr;5(4):565-572. PMID: 18362024 | PDF

Authors: Matthew Jolley, Jeroen Stinstra, Steve Pieper, Rob Macleod, Dana H. Brooks, Frank Cecchin, John K. Triedman

Institution: Department of Cardiology, Children’s Hospital Boston, Boston, MA, USA.

Background/Purpose: Use of implantable cardiac defibrillators (ICDs) in children and patients with congenital heart disease is complicated by body size and anatomy. A variety of creative implantation techniques has been used empirically in these groups on an ad hoc basis. OBJECTIVE: To rationalize ICD placement in special populations, we used subject-specific, image-based finite element models (FEMs) to compare electric fields and expected defibrillation thresholds (DFTs) using standard and novel electrode configurations. METHODS: FEMs were created by segmenting normal torso computed tomography scans of subjects ages 2, 10, and 29 years and 1 adult with congenital heart disease into tissue compartments, meshing, and assigning tissue conductivities. The FEMs were modified by interactive placement of ICD electrode models in clinically relevant electrode configurations, and metrics of relative defibrillation safety and efficacy were calculated. RESULTS: Predicted DFTs for standard transvenous configurations were comparable with published results. Although transvenous systems generally predicted lower DFTs, a variety of extracardiac orientations were also predicted to be comparably effective in children and adults. Significant trend effects on DFTs were associated with body size and electrode length. In many situations, small alterations in electrode placement and patient anatomy resulted in significant variation of predicted DFT. We also show patient-specific use of this technique for optimization of electrode placement. CONCLUSION: Image-based FEMs allow predictive modeling of defibrillation scenarios and predict large changes in DFTs with clinically relevant variations of electrode placement. Extracardiac ICDs are predicted to be effective in both children and adults. This approach may aid both ICD development and patient-specific optimization of electrode placement. Further development and validation are needed for clinical or industrial utilization.

Funding:

• NIH P41 RR12557
• NIH P41 RR13218
• NIH T32 HL07572
• CIMIT

Publication: Comput Aided Surg. 2007 Nov;12(6):311-24. PMID: 18066947 | PDF

Authors: Raúl San José Estépar, Nicholas Stylopoulos, Randy Ellis, Eigil Samset, Carl-Fredrik Westin, Christopher Thompson, Kirby Vosburgh

Institution: Department of Radiology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.

Background/Purpose: Scarless surgery is an innovative and promising technique that may herald a new era in surgical procedures. We have created a navigation system, named IRGUS, for endoscopic and transgastric access interventions and have validated it in in vivo pilot studies. Our hypothesis is that endoscopic ultrasound procedures will be performed more easily and efficiently if the operator is provided with approximately registered 3D and 2D processed CT images in real time that correspond to the probe position and ultrasound image. Materials and Methods: The system provides augmented visual feedback and additional contextual information to assist the operator. It establishes correspondence between the real-time endoscopic ultrasound image and a preoperative CT volume registered using electromagnetic tracking of the endoscopic ultrasound probe position. Based on this positional information, the CT volume is reformatted in approximately the same coordinate frame as the ultrasound image and displayed to the operator. Results: The system reduces the mental burden of probe navigation and enhances the operator's ability to interpret the ultrasound image. Using an initial rigid body registration, we measured the mis-registration error between the ultrasound image and the reformatted CT plane to be less than 5 mm, which is sufficient to enable the performance of novice users of endoscopic systems to approach that of expert users. Conclusions: Our analysis shows that real-time display of data using rigid registration is sufficiently accurate to assist surgeons in performing endoscopic abdominal procedures. By using preoperative data to provide context and support for image interpretation and real-time imaging for targeting, it appears probable that both preoperative and intraoperative data may be used to improve operator performance.

Funding:

• NIH P41-RR13218
• CIMIT

Publication: Journal of Morphology 2007; 268:243-253. PMID: 17278134 | PDF. See also 3D Slicer: The Tutorial Part V.

Authors: Farke, A. A.

Institution: Department of Anatomical Sciences, Stony Brook University, N.Y.

Background/Purpose: The frontal sinuses of bovid mammals display a great deal of diversity, which has been attributed to both phylogenetic and functional influences. In-depth study of the hartebeest (Alcelaphus buselaphus), a large African antelope, reveals a number of previously undescribed details of frontal sinus morphology. In A. buselaphus, the frontal sinuses conform closely to the shape of the frontal bone, filling nearly the entire element. However, the horncores are never extensively pneumatized, contrasting with the condition seen in many other bovids. This evidence is inconsistent with the hypothesis that sinuses are opportunistic pneumatizing agents, suggesting that phylogenetic factors also play a role in determining sinus size. Both cranial sutures and neurovasculature appear to constrain the growth of sinuses in part. In turn, the sinus also affects the growth of the parietal; apparently this element is not truly pneumatized by the sinus in most cases, but the bone’s shape changes under the influence of the sinus. Furthermore, the sinuses present relatively few struts when compared with the sinuses of some other bovids, such as Ovis. By adapting methods previously developed for measuring structural parameters of trabecular bone, it is possible to quantify certain aspects of sinus morphology. These include the number of bony struts within the sinus, the spacing of these struts, and the size of individual cavities within the sinus. Some differences in the number of struts are evident between subspecies. Similarly, significant differences occur in the relative number of struts between male and female A. buselaphus, which may be related to behavior. The volume of the sinus is strongly correlated with the size of the frontal, but less so with overall cranial size. This finding illustrates the importance of choosing variables carefully when comparing sinus sizes and growth between species.

Publication: Proceedings of ACCAS2007, #P110064

Authors: Hong J, Matsumoto N, Ouchida R, Komune S, Hashizume M

Institution: Redox Navi Institute, Kyushu University, Japan.

Background/Purpose: Image-guided surgery has been established particularly in ear, nose, throat (ENT) surgery that requires precise approach in small and complicated anatomy. During the surgery, the registration between the patient and the radiographic images must be maintained regardless of the patient movement. In this study, relative position and orientation of the surgical instrument is calculated referring to the moving patient position. Since the system does not directly handle the 3-D volume data, real-time update of 3-D navigational view is possible. The proposed method also keeps recording the surgical drill position while tracking it. With these digitized data, the temporal bone resection area is computed with several rule-based image processing. Finally, virtual CT images are constructed, and presented for the surgeon to understand and evaluate the current operation intraoperatively by observing their familiar CT images. The aim of this study is to develop and evaluate a novel otologic navigation system supporting patient motion compensation and intraoperative virtual CT construction.

Publication: Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):969-77. PMID: 18044662 | PDF

Authors: N Archip, S Tatli, PR Morrison, F Jolesz, SK Warfield, SG Silverman

Institution: Department of Radiology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.

Background/Purpose: In the United States, unenhanced CT is currently the most common imaging modality used to guide percutaneous biopsy and tumor ablation. The majority of liver tumors such as hepatocellular carcinomas are visible on contrast-enhanced CT or MRI obtained prior to the procedure. Yet, these tumors may not be visible or may have poor margin conspicuity on unenhanced CT images acquired during the procedure. Non-rigid registration has been used to align images accurately, even in the presence of organ motion. However, to date, it has not been used clinically for radiofrequency ablation (RFA), since it requires significant computational infrastructure and often these methods are not sufficient robust. We have already introduced a novel finite element based method (FEM) that is demonstrated to achieve good accuracy and robustness for the problem of brain shift in neurosurgery. In this current study, we adapt it to fuse pre-procedural MRI with intra-procedural CT of liver. We also compare its performance with conventional rigid registration and two non-rigid registration methods: b-spline and demons on 13 retrospective datasets from patients that underwent RFA at our institution. FEM non-rigid registration technique was significantly better than rigid (p<10-5), non-rigid b-spline (p<10- 4) and demons (p<10-4) registration techniques. The results of our study indicate that this novel technology may be used to optimize placement of RF applicator during CT-guided ablations.

Funding:

• NSF ITR 0426558
• NIH R03 EB006515
• NIH U41 RR019703
• NIH P01 CA067165
• NIH R01 021885

Publication: Proceedings of the 29th Annual International Conference of the IEEE EMBS, 2007. | PDF

Authors: Anquez, J., Angelini, E., Bloch, I., Merzoug, V., Bellaiche-Millischer, A.E., Adamsbaum, C.

Institution: Signal and Image Processing Department, GET - Telecom Paris, France.

Background/Purpose: Fetal magnetic resonance imaging (MRI) has been gaining interest over the last two decades. Current fast MRI sequences provide imaging data of the whole uterus in less than 20 seconds, avoiding fetal motion related artifacts without any maternal or fetal sedation. MRI has proved to be a useful adjunct to echographic screening for prenatal diagnosis. However, MRI volumetric data is still mainly interpreted on 2D slices and 3D applications remain limited. In this paper, we discuss the qualities of the SSFP MRI sequences to provide adequate data for 3D segmentation and modeling of the fetus. Potential exploitations of 3D segmentation and derived anatomical models cover several domains: biometric and morphologic clinical studies, quantitative longitudinal studies of normal and abnormal fetus developments, direct visualization of the overall fetus body and simulations in different fields (surgery, radiation dosimetry,...).

Publication: Am J Obstet Gynecol. 2007 Mar;196(3):251.e1-5. PMID: 17346542 | PDF

Authors: Margulies RU, Huebner M, DeLancey JO.

Institution: Pelvic Floor Research Group, University of Michigan, Ann Arbor, MI, USA.

Background/Purpose: This project sought to identify and to describe the anatomical connections affected by levator ani defects involving the pubovisceral portion of the muscle. STUDY DESIGN: Fourteen magnetic resonance scans of women with unilateral levator defects were selected. The missing muscle mapping technique was used to characterize the absent muscle. Normal muscle was visualized and compared with the contralateral side. Using a 3D Slicer, the outline of the intact muscle was traced; models of this muscle and surrounding structures were generated. RESULTS: The missing muscle originates from the posterior pubic bone and extends laterally over the obturator internus muscle; it inserts into the vaginal wall, perineal body, and the intersphincteric space. Architectural distortion, with an asymmetric lateral spilling of the vagina was present in 50% of women. The defect was right sided in 71% of patients. CONCLUSION: The origin and insertion points of the damaged portion of the levator ani muscle were identified.

Funding:

• National Institute of Child Health and Human Development Grants P50 HD 44406 and R01 HD 38665
• National Institute of Diabetes and Digestive and Kidney Diseases R01 DK 051405
• German Research Foundation, Grant HU1502/1-1.

Publication: Int J Med Robot. 2007 Mar;3:82-8. PMID: 17441030 | PDF

Authors: Reisner LA, King BW, Klein MD, Auner GW, Pandya AK.

Institution: Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI, USA.

Background/Purpose: In this study we investigated the integration of a Raman spectroscopy-based biosensor with an image-guided surgery system. Such a system would provide a surgeon with both a diagnosis of the tissue being analysed (e.g. cancer) and localization information displayed within an imaging modality of choice. This type of mutual and registered information could lead to faster diagnoses and enable more accurate tissue resections. METHODS: A test bed consisting of a portable Raman probe attached to a passively articulated mechanical arm was used to scan and classify objects within a phantom skull. RESULTS: The prototype system was successfully able to track the Raman probe, classify objects within the phantom skull, and display the classifications on medical imaging data within a virtual reality environment. CONCLUSION: We discuss the implementation of the integrated system, its accuracy and improvements to the system that will enhance its usefulness and further the field of sensor-based computer-assisted surgery.

Funding:

• Endowment for Surgical Research (ENSURE) at the Children’s Research Center of Michigan.

Publication: Int J CARS (2007) 2:65–73. | PDF

Authors: Georgi Diakov, Wolfgang Freysinger

Institution: 4D Visualization Laboratory, University Clinic of Oto-, Rhino-, Laryngology, Innsbruck Medical University, Innsbruck, Austria

Background/Purpose: An initialization-free approach for perioperative registration in functional endoscopic sinus surgery (FESS) is sought. The quality of surgical navigation relies on registra- tion accuracy of preoperative images to the patient. Although landmark-based registration is fast, it is prone to human oper- ator errors. This study evaluates the accuracy of two well- known methods for segmentation of the occipital bone from CT-images for use in surgical 3D-navigation.

Funding:

• Jubilee Funds of the Austrian National Bank, Grant# 9318.

Publication: J Theor Biol. 2007 Jan 7;244(1):96-107. PMID: 16949103 | PDF

Authors: Zhang L, Athale CA, Deisboeck TS.

Institution: Complex Biosystems Modeling Laboratory, Massachusetts General Hospital

Background/Purpose: Related also to efforts within the Center for the Development of a Virtual Tumor, CViT (http://www.cvit.org), our research here (http://biosystems.mit.edu) focuses on developing multi-scale and multi-resolution (brain) cancer models. Using a hybrid 3D agent-based modeling platform we connect gene-protein interaction maps on the molecular and single cell level (Figure 1, left) up to the volumetric tumor scale of clinical MR-images. For the latter, we plan on using Slicer for segmentation of tumor-affected areas and 3D reconstruction of tumor volume and surface. Figure 1, right depicts a first step towards this approach where the yellow points depict the 3D surface reconstruction of a T1+Gd MRI while the blue and red points represent virtual tumor cells in attempt to match the real data points. Amongst the more challenging steps is the translation of these 2D in vivo imaging data onto our in silico lattices.

Funding:

• NIH CA 085139
• NIH CA 113004

Authors: Kilian Pohl in collaboration with Steve Pieper, Kirby Vosburgh, and Barnabas Takacs.

Background/Purpose: Dr. Pohl's research involves developing an automatic segmentation approach identifying major anatomical compartments from torso CT scans. Using 3D Slicer, he developed a procedure for automatically segmenting the body, bone structures, lungs, and hart from CT images (see figure). The method iterates between the identification of anatomical structures and the registration of an “atlas” to the CT data set of the subject. The atlas is based on CT data set, which we call template, and a label map that already identifies the structures of interest in the template. In the first iteration, the template with the segmentation of the body is mapped onto the CT data set of the subject. This results in a very accurate segmentation of the subject’s body. The method then combines the segmentation of the body and the CT images of the subject to identify the lungs and bone structures. In the second iteration, the method maps the atlas specific label map of body, bones, and lungs to the corresponding label map of the subject. The segmented structures are then used as a "coordinate system" used for the identification of the remaining anatomical compartments.

Funding:

• SBIR SNC06C0003 TATRC/CIMIT for Image Guided FAST Ultrasound.

Publication: Proceedings of the 76th Annual Meeting of the American Association of Physical Anthropologists March 2007. | PDF

Authors: L.N. Butaric, D.C. Broadfield, R.C. McCarthy

Institution: Department of Anthropology, Texas A&M University

Background/Purpose: Previous research suggests that nasal cavity volume (NCV), thought to be related to climate, is inversely correlated with maxillary sinus volume (MSV). According to this hypothesis, changes in nasal cavity size and shape reflect physiological needs, such as warming and humidifying inspired air. Owing to volumetric constraints in the mid-face, relative increases in NCV are hypothesized to result in concomitant decreases in MSV, respectively. To test this hypothesis thirty-nine dried adult human crania from seven different climatic regions were examined using computerized tomography (CT) scans. Significant differences in MSV and NCV between populations were identified using Analysis of Variance (ANOVA). In addition, least-squares and reduced major axis (RMA) regression analyses were performed to test the scaling relationships between MSV, NCV and several cranial size variables. Contrary to previous studies, results indicate that MSV and NCV are not significantly correlated. RMA analyses indicate that NCV, but not MSV, scales isometrically with skull size. Finally, post hoc ANOVA results identify significant differences between human populations for MSV that do not follow climatic or environmental trends. These results suggest that (1) it is unlikely that NCV and MSV compete for space in the mid-face, (2) NCV is largely a byproduct of skull size, and (3) NCV and MSV may not be as closely tied to climate as previously thought. Additional genetic and epigenetic factors need to be considered regarding the structure and function of the human maxillary sinus.

Publication: Chest. 2007 Feb;131(2):424-31. PMID: 17296643 | PDF

Authors: Hersh CP, Washko GR, Jacobson FL, Gill R, Estepar RS, Reilly JJ, Silverman EK.

Institution: Channing Laboratory, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA.

Background/Purpose: Appropriateness for lung volume reduction surgery is often determined based on the results of high-resolution CT (HRCT) scanning of the chest. At many centers, radiologists and pulmonary physicians both review the images, but the agreement between readers from these specialties is not known. METHODS: Two thoracic radiologists and three pulmonologists retrospectively reviewed the HRCT scans of 30 patients with emphysema involved in two clinical studies at our institution. Each reader assigned an emphysema severity score and assessed upper lobe predominance, using a methodology similar to that of the National Emphysema Treatment Trial. In addition, the percentage of emphysema at -910 Hounsfield units was objectively determined by density mask analysis. RESULTS: For the emphysema severity scores, (Spearman) correlation between readers ranged from 0.59 (p = 0.0005) to 0.87 (p < 0.0001), with generally stronger correlations among readers from the same medical specialty. Emphysema severity scores were significantly correlated with prebronchodilator and postbronchodilator spirometry findings, as well as with density mask analysis. In the assessment of upper lobe predominance, kappa statistics for agreement ranged from 0.20 (p = 0.4) to 0.60 (p = 0.0008). Examining all possible radiologist-pulmonologist pairs, the two readers agreed in their assessments of emphysema distribution in 75% of the comparisons. Readers agreed on upper lobe-predominant disease in 9 of the 10 patients in which regional density mask analysis clearly showed upper lobe predominance. CONCLUSIONS: In a group of patients with varying emphysema severity, interobserver agreement in the determination of upper lobe-predominant disease was poor. Agreement between readers tended to be better in cases with clear upper lobe predominance as determined by densitometry.

Funding:

• HL075478/HL/NHLBI NIH HHS/United States
• HL080242/HL/NHLBI NIH HHS/United States
• HL68926/HL/NHLBI NIH HHS/United States
• HL71393/HL/NHLBI NIH HHS/United States

Publication: Proceedings of the International Conference and Exhibition in Virtual Reality 2007; 277-278. | PDF

Authors: Brady W. King, Luke A. Reisner, Michael D. Klein, Gregory W. Auner, Abhilash K. Pandya

Institution: Wayne State University, Detroit, Michigan, USA

Background/Purpose: The visualization for our image-guided surgery system is implemented using 3D Slicer, an open-source application for displaying medical data. 3D Slicer provides a virtual reality environment in which various imaging modalities (e.g. CT or MRI data) can be presented. The software includes the ability to display the locations of objects with respect to 3D models that are derived from segmentation of the medical imaging.

We modified 3D Slicer in several ways to adapt it to our application. First, we developed a TCP/IP interface that receives the tracking data for the MicroScribe and displays its position in the VR environment relative to the medical imaging data. This allows us to track the Raman probe in real-time. Second, we developed a way to place colored markers that indicate tissue/material classification on the medical imaging data. The combination of these modifications enables us to denote the location and classification of tissue/material scanned with the probe in near-real-time.

Publication: National Science Foundation (NSF) Discoveries - Brain Surgery: It Really Is Brain Surgery, August 31, 2007.

Authors: Nikos Chrisochoides

Institution: College of William and Mary

Background/Purpose: In essence, the William and Mary team provides the surgical team with a dynamic computer model of the patient's brain. In clinical trials, Chrisochoides says his team can render a new model in six or seven minutes, but hopes to be able to do so in under two minutes. More...

Funding:

• National Science Foundation Award#0521381

Publication: Biomedical Computation Review Spring 2007 pp. 16-24. | PDF

Author: Kristin Cobb

Publication: Med Bio Eng Comput. 2006 Dec; 44(12):1127-1134. PMID: 17102954

Authors: Hong J, Nakashima H, Konishi K, Ieiri S, Tanoue K, Hashizume M

Institution: Redox Navi Institute, Kyushu University, Japan.

Background/Purpose: Surgical navigation systems can contribute to abdominal interventions such as radiofrequency ablation (RFA) or percutaneous ethanol injection therapy (PEIT) for liver tumours. Until now, typical abdominal interventions have been performed using the US guidance approach. Identification of the lesion by these methods has often been difficult, especially when tumours were small and US images were unclear. To improve the treatment with better lesion identification, 3D navigation based on MRI or CT is crucial. Particularly, MRI-based navigation systems have been preferred in respect of avoidance of ionizing radiation. To our knowledge, this is the first trial of abdominal needle insertion intervention under local anaesthesia using simultaneous MRI and US navigation. To accomplish this purpose, the semi-automatic fiducial registration is required. While scanning the abdominal area and using the optical tracking system, partial loss of the markers often occurs, leading to the prolongation of the limited intervention time. The proposed method combats this problem. In this paper, we elucidate whether the MRI and US integrated navigation assists in reliable needle insertion and reduce the time required to determine the needle insertion path in abdominal interventions.

Publication: South African Journal of Science. 2006;102(11-12):513-517. | PDF

Authors: SMITH Tanya M., OLEJNICZAK Anthony J., TAFFOREAU Paul, REID Donald J., GRINE Fredrick E., HUBLIN Jean-Jacques

Institution: Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

Background/Purpose: One highly debated issue in palaeoanthropology is that of modern human origins, particularly the issue of when 'anatomically modern humans' (AMH) from the African Middle Stone Age became fully modern. While studies of cranial and external dental morphology suggest a modern transition occurred 150 000-200 000 years ago, little is known about dental development or enamel thickness in AMH. Studies of early members of the genus Homo suggest that the modern, prolonged condition of tooth growth arose late in human evolution, and that the enamel thickness of earlier hominins may not be homologous to the modern condition. This study represents the first integrated investigation of molar crown enamel thickness, volume, and development in fossil hominins, aimed at determining whether differences between AMH and living populations can be detected in these traits. Using high-resolution micro-computed tomography, we demonstrate similarities in enamel thickness and crown volumes between fossil and modern populations. Additionally, long-period growth line numbers and estimates of crown formation times for AMH molars fall within modern human ranges. These findings suggest that tooth structure and growth have remained constant for more than 60 000 years, despite the known geographical, technological, and ecological diversity that characterizes later stages of human evolution.

Publication: Poster Presentation at the 2007 American Thoracic Society International Conference

Authors: RD McEvoy, MK Ryan, PG Catcheside, M Jakab, A Malhotra, MR Sage, R Valentine, DP White

Institution: Adelaide Institute for Sleep Health, Repatriation General Hospital, SA Australia.

Background/Purpose: For the same BMI female OSA patients tend to have less severe sleep disordered breathing than male OSA patients. This study investigates features of upper airway anatomy that may contribute to this difference. METHOD: Male (n=6) and female (n=9) patients matched for age [mean(SD); men 56.5(5.7), women 55.3(6.2) yrs] and BMI [35.2(3.4), 34.3 (3.0) kg/m²], who had previously been diagnosed with OSA (AHI>30/h), and adherent with CPAP for >3 months were studied. T1 weighted magnetic resonance imaging of the upper airway and surrounding tissues was performed and analyzed (3D Slicer) to determine airway, soft tissue and bony dimensions. RESULTS: The oropharyngeal bony vault volume was greater in males after normalizing for height (1.2(0.1) vs 0.97(0.1), mls/cm, p=0.001). Men had greater neck circumference (45.3(4.3) vs 39.5(4.5) cm, p=0.026) and longer pharyngeal airways (75.2(8.3) vs 64.6(9.5) mm, p=0.042) compared to women. Pharyngeal airway volume and minimum CSA were not different between the genders. In the mid sagittal plane, the tongue CSA was greater in men before and after (36.4(1.4) vs 32.6(3.5) mm²/mm, p=0.01) normalizing for bony vault dimensions. In data collected to date, AHI was not different between males and females (55(12) vs 62(21) events/h). CONCLUSIONS: These preliminary data suggest that male OSA patients have greater oropharyngeal bony vault volume than female patients; a larger tongue (normalized for bony vault dimensions) and a longer pharyngeal airway. These findings may have implications for the male predisposition for OSA.

Funding:

• Royal Australian and New Zealand College of Radiologists

Publication: PowerPoint Presentation PDF

Authors: Derek Karssenberg and John Bridge

Institution: Utrecht University, the Netherlands and Binghamton University, NY, USA.

Publication: PowerPoint Presentation PPT

Author: Martha Liliana Mora V.

Institution: Rey Juan Carlos University, Madrid, Spain.

Publication: Obstet Gynecol. 2006 Oct;108(4):879-83. PMID: 17012449 | PDF

Authors: Hsu Y, Chen L, Huebner M, Ashton-Miller JA, DeLancey JO.

Institution: University of Michigan, Ann Arbor, Michigan, USA

Background/Purpose: Compare levator ani cross-sectional area as a function of prolapse and muscle defect status. METHODS: Thirty women with prolapse and 30 women with normal pelvic support were selected from an ongoing case-control study of prolapse. For each of the two groups, 10 women were selected from three categories of levator defect severity: none, minor, and major identified on supine magnetic resonance scans. Using those scans, three-dimensional (3D) models of the levator ani muscles were made using a modeling program (3D Slicer), and cross-sections of the pubic portion were calculated perpendicular to the muscle fiber direction using another program, I-DEAS. An analysis of variance was performed. RESULTS: The ventral component of the levator muscle of women with major defects had a 36% smaller cross-sectional area, and women with minor defects had a 29% smaller cross-sectional area compared with the women with no defects (P < .001). In the dorsal component, there were significant differences in cross-sectional area according to defect status (P = .03); women with major levator defects had the largest cross-sectional area compared with the other defect groups. For each defect severity category (none, minor, major), there were no significant differences in cross-sectional area between women with and those without prolapse. CONCLUSION: Women with visible levator ani defects on magnetic resonance imaging had significantly smaller cross-sectional areas in the ventral component of the pubic portion of the muscle compared with women with intact muscles. Women with major levator ani defects had larger cross-sectional areas in the dorsal component than women with minor or no defects.

Funding:

• NIH R01 HD-38665
• DGF HU1502

Publication: Radiology. 2006 Oct;241(1):243-50. PMID: 16928977 | PDF

Authors: Ivan Bricault, Ron Kikinis, Paul R Morrison, Eric Vansonnenberg, Kemal Tuncali, Stuart G Silverman

Institution: Department of Radiology, University Hospital Michallon, Grenoble, France

Background/Purpose: The purpose of this pilot study was to determine retrospectively the diagnostic performance of a computer-aided three-dimensional (3D) analytic tool for assessing local recurrences of liver metastases by quantifying shape changes in ablated tumors on computed tomographic (CT) scans for follow-up of radiofrequency (RF) ablation. Positron emission tomographic and long-term CT follow-up images were reference standards. Fifty-six follow-up CT scans of 12 liver metastases (mean size, 4.0 cm) in nine patients treated with RF ablation were retrospectively analyzed. After the 1st month following RF ablation, the 3D analytic tool helped quantify ablated tumor shape variations and revealed recurrences even in the absence of abnormal enhancement (sensitivity, seven of seven; specificity, three of five). The 3D tool would have revealed a recurrence before it was reported clinically in two patients. Although results are preliminary, a 3D analytic tool based on shape may be useful in assessing RF ablation results.

Funding:

• Study grant from the French Radiological Society

Publication: Int Conf Med Image Comput Comput Assist Interv. 2006;9(Pt 2):209-16. PMID: 17354774 | PDF

Authors: Ayelet Akselrod-Ballin, Meirav Galun, Moshe John Gomori, Ronen Basri, and Achi Brandt

Institution: Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel and Department of Radiology, Hadassah University Hospital, Jerusalem, Israel

Background/Purpose: This study presents a novel automatic approach for the identification of anatomical brain structures in magnetic resonance images (MRI). The method combines a fast multiscale multi-channel three dimensional (3D) segmentation algorithm providing a rich feature vocab ulary together with a support vector machine (SVM) based classifier. The segmentation produces a full hierarchy of segments, expressed by an irregular pyramid with only linear time complexity. The pyramid provides a rich, adaptive representation of the image, enabling detection of various anatomical structures at different scales. A key aspect of the approach is the thorough set of multiscale measures employed throughout the segmentation process which are also provided at its end for clinical analysis. These features include in particular the prior probability knowl- edge of anatomic structures due to the use of an MRI probabilistic atlas. An SVM classifier is trained based on this set of features to identify the brain structures. We validated the approach using a gold standard real brain MRI data set. Comparison of the results with existing algorithms displays the promise of our approach.

Funding:

• Grant #2002/254 Israel Institute of Technology
• IST-2002-506766 European Commission Project

Publication: PDF

Authors: Eleonora Tommasi and Giorgio De Nunzio

Institution: Departments of Physics and Material Science, University of Lecce, Italy

Background/Purpose: We implemented a piece of software to segment lung tissue in CT thoracic images. We gave particular attention to the study of the ilhus pulmonis (region of entrance of bronchi and vessels in the lung parenchima). It is a delicate region in segmentation. We used Slicer to visualize the different steps of the algorithm, checking their correctness. Through a segmentation technique, known as “region growing”, we obtained the delineation of the respiratory apparatus domain in the CT scans. This algorithm is completely three-dimensional. Its output consists in the 3D mask of the respiratory apparatus. We used 3D Slicer to visualize it. Then through an alternative version of region growing, based on a wavefront simulation algorithm, we obtained the segmentation of the external bronchi. We also used the opacity proprieties to put in evidence the internal structures of lungs (such as vessels).

Author: Trent M. Guess

Institution: Mechanical Engineering, University of Missouri-Kansas City

Background/Purpose:

1. Develop computationally efficient algorithms that capture tibio-femoral-menisci articulations through neural networks that learn from computationally intensive finite-element tissue models.
2. Evaluate tissue interdependencies of the knee during ambulatory activity including the effect of modified menisci properties and/or geometries on tibio-femoral contact pressures.

Funding:

• National Science Foundation, Grant Number 506297, under the IMAG program for Multiscale Modeling.

Researchers: Yehoshua Y. Zeevi, Emil Saucan and Eli Appleboim

Institution: Department of Electrical-Engineering, Technion-Israel Institute of Technology, Haifa, Israel.

Description: CT/MRI-scans of human brain-cortex/colon are flattened in a quasi-isometric manner in order to keep angles/length/area as minimally distorted as possible. 3D-surfaces are created out of real data scans, using 3D Slicer .

Funding:

• Viterbi Post Doc. fellowship Ollendorf Minerva Center Fund
• Technion V.P. Fund for Promotion of Research at the Technion

Publication: RSNA 2006;

Authors: P Mongkolwat, T Lechner, A Kogan, S Talbot, B Johnson, D S Channin

Institution: Imaging Informatics Section, Northwestern University, Chicago, IL 60611, USA

Background/Purpose: Abstract: while providing clinical feedback to the basic sciences. In imaging informatics, this means enabling collaborations between radiologists and computer scientists. Commercial workstations do not allow for experimentation nor do they evolve fast enough. Research imaging packages, while innovative, do not provide for clinical activities or regulatory compliance. We added IHE workflow functionality, hanging protocols and other clinical functions to the Slicer research platform. We leveraged the functionality and methodology of the Insight and Visualization Toolkits, and the DCM4CHE tools. A research mode allows for the evaluation of experimental algorithms against a PACS while protecting patient confidentiality. This combined functionality allows researchers to develop algorithms against clinical cases while at the same allowing clinicians to explore and validate these developments.

Publication: Med Image Anal. 2006 Dec;10(6):841-9. PMID: 16965928 | PDF

Authors: Caan MW, Vermeer KA, van Vliet LJ, Majoie CB, Peters BD, den Heeten GJ, Vos FM.

Institution: Quantitative Imaging Group, Delft University of Technology, Delft, The Netherlands.

Background/Purpose: A technique called 'shaving' is introduced to automatically extract the combination of relevant image regions in a comparative study. No hypothesis is needed, as in conventional pre-defined or expert selected region of interest (ROI)-analysis. In contrast to traditional voxel based analysis (VBA), correlations within the data can be modeled using principal component analysis (PCA) and linear discriminant analysis (LDA). A study into schizophrenia using diffusion tensor imaging (DTI) serves as an application. Conventional VBA found a decreased fractional anisotropy (FA) in a part of the genu of the corpus callosum and an increased FA in larger parts of white matter. The proposed method reproduced the decrease in FA in the corpus callosum and found an increase in the posterior limb of the internal capsule and uncinate fasciculus. A correlation between the decrease in the corpus callosum and the increase in the uncinate fasciculus was demonstrated.

Funding:

• BSIK grant from the Dutch Ministry of Education, Culture and Science (OC&W)
• ICT innovation program of the Ministry of Economic Affairs (EZ).

Publication: Neuroimage. 2006 Jul 1;31(3):1116-28. PMID: 16545965 | PDF

Authors: Yushkevich PA, Piven J, Hazlett HC, Smith RG, Ho S, Gee JC, Gerig G.

Institution: Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania, PA 19104-6274, USA.

Background/Purpose: Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.

Funding:

• MH 064065/MH/NIMH NIH HHS/United States
• MH 64580/MH/NIMH NIH HHS/United States
• P0 467-MZ-202446-1/PHS HHS/United States
• P01 EB002779/EB/NIBIB NIH HHS/United States
• R01 MH61696/MH/NIMH NIH HHS/United States

Publication: J Anat. 2006 Jun; 208(6):659-670. PMID: 16761969 | PDF

Authors: Carlson KJ, Patel BA.

Institution: Department of Anatomical Sciences, School of Medicine, Stony Brook University, USA.

Background/Purpose: Bone mineral density is directly proportional to compressive strength, which affords an opportunity to estimate in vivo joint load history from the subchondral cortical plate of articular surfaces in isolated skeletal elements. Subchondral bone experiencing greater compressive loads should be of relatively greater density than subchondral bone experiencing less compressive loading. Distribution of the densest areas, either concentrated or diffuse, also may be influenced by the extent of habitual compressive loading. We evaluated subchondral bone in the distal radius of several primates whose locomotion could be characterized in one of three general ways (quadrupedal, suspensory or bipedal), each exemplifying a different manner of habitual forelimb loading (i.e. compression, tension or non-weight-bearing, respectively). We employed computed tomography osteoabsorptiometry (CT-OAM) to acquire optical densities from whichfalse-colour maps were constructed. The false-colour maps were used to evaluate patterns in subchondral density (i.e. apparent density). Suspensory apes and bipedal humans had both smaller percentage areas and less well-defined concentrations of regions of high apparent density relative to quadrupedal primates. Quadrupedal primates exhibited a positive allometric effect of articular surface size on high-density area, whereas suspensory primates exhibited an isometric effect and bipedal humans exhibited no significant relationship between the two. A significant difference between groups characterized by predominantly compressive forelimb loading regimes vs. tensile or non-weight-bearing regimes indicates that subchondral apparent density in the distal radial articular surface distinguishes modes of habitually supporting of body mass.

Funding:

• Sigma Xi Grants-In-Aid of Research to B.A.P.

Publication: Obstet Gynecol. 2006 May;107(5):1064-9. PMID: 16648412 | PDF

Authors: Rebecca U. Margulies, Md, Yvonne Hsu, Md, Rohna Kearney, Mrcog, Tamara Stein, Phd, Wolfgang H. Umek, Md, and John O. L. DeLancey, Md

Institution: University of Michigan, Ann Arbor, Michigan; University College Hospital, London, United Kingdom; and Medical University Vienna, Vienna, Austria.

Background/Purpose: Identify and describe the separate appearance of 5 levator ani muscle subdivisions seen in axial, coronal, and sagittal magnetic resonance imaging (MRI) scan planes. METHODS: Magnetic resonance scans of 80 nulliparous women with normal pelvic support were evaluated. Characteristic features of each Terminologia Anatomica–listed levator ani component were determined for each scan plane. Muscle component visibility was based on pre- established criteria in axial, coronal, and sagittal scan planes: 1) clear and consistently visible separation or 2) different origin or insertion. Visibility of each of the levator ani subdivisions in each scan plane was assessed in 25 nulliparous women.RESULTS: In the axial plane, the puborectal muscle can be seen lateral to the pubovisceral muscle and decussating dorsal to the rectum. The course of the puboperineal muscle near the perineal body is visualized in the axial plane. The coronal view is perpendicular to the fiber direction of the puborectal and pubovisceral muscles and shows them as “clusters” of muscle on either side of the vagina. The sagittal plane consistently demonstrates the puborectal muscle passing dorsal to the rectum to form a sling that can consistently be seen as a “bump.” This plane is also parallel to the pubovisceral muscle fiber direction and shows the puboperineal muscle. CONCLUSION: The subdivisions of the levator ani muscle are visible in MRI scans, each with distinct morphology and characteristic features.

Funding:

• NICHD P50 HD 44406
• R01 HD 38665

Publication: Arch Ital Urol Androl. 2006 Mar;78(1):23-4. PMID: 16752884

Authors: Braticevici B, Onu M, Bengus F.

Institution: Clinical Hospital, Bucharest, Romania.

Background/Purpose: Image guided-surgery systems facilitates surgical planning phases of endoscopic procedures. In this paper, we used a software package for 3D surface model generation and vizualization of the urinary bladder, based on magnetic resonance (MR) cross sectional images of the pelvis. The patients group consisted in 6 patients diagnosed with urinary bladder tumour. They were submitted to MRI exam. Twelve consecutive cross sectional images of the pelvis were aquired (TR (repetition time) = 600 msec, TE (echo time) = 19 msec, slice thickness = 6 divided by 7 mm, FOV (field of view) = 36 cm. All these images were transferred to a personal computer running the 3D Slicer software. We obtained, for each patient, a 3D model of the pelvis including the urinary bladder. In This way, the surgical enviroment was simulated and we are able to investigate the bladder by virtual cystoscopy. The virtual endoscopy may be used as a tool in the preoperative training and in surgical planning.

Publication: Int J Gynaecol Obstet. 2006 Mar;92(3):234-41. PMID: 16442111 | PDF

Authors: Chen L, Hsu Y, Ashton-Miller JA, DeLancey JO

Institution: Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2125, USA.

Background/Purpose: Develop a method to quantify the cross-sectional area of the pubic portion of the levator ani muscle, validate the method in women with unilateral muscle defects, and report preliminary findings in those women. METHOD: Multi-planar proton density magnetic resonance images of 12 women with a unilateral defect in the pubic portion of their levator ani were selected from a larger study of levator ani muscle anatomy in women with and without genital prolapse. Three-dimensional bilateral models of the levator ani were reconstructed (using 3D Slicer, version 2.1b1) and divided into iliococcygeal and pubic portions. Muscle cross-sectional areas were calculated at four equally spaced locations perpendicular to a line drawn from the pubic origin to the visceral insertion using the I-DEAS computer modeling software. RESULTS: The cross-sectional area of the muscle on the side with the defect was smaller than the normal side at all the four locations. The average bilateral difference was up to 81% at location 1 (nearest pubic origin). Almost all of the volume difference (13.7%, P=0.0004) was attributable to a reduction in the pubic portion (24.6%, P<0.0001), not the iliococcygeal portion (P=0.64), of the muscle. CONCLUSIONS: A method was developed to quantify cross-sectional area of the pubic portion of the levator ani perpendicular to the intact muscle direction. Significant bilateral cross-sectional area differences were found between intact and defective muscles in women with a unilateral defect.

Funding:

• NICHD R01 HD-38665

Publication: J Oral Maxillofac Surg. 2006 Feb;64(2):259-64. PMID: 16413898 | PDF

Authors: Ritter L, Yeshwant K, Seldin EB, Kaban LB, Gateno J, Keeve E, Kikinis R, Troulis MJ

Institution: Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital, Boston, MA, USA.

Background/Purpose: The purpose of this study was to determine the range of fixed trajectory curvilinear distraction devices required to correct a variety of severe mandibular deformities. MATERIALS AND METHODS: Preoperative computed tomography (CT) scans from 18 patients with mandibular deformities were imported into a CT-based software program (Osteoplan). Three-dimensional virtual models of the individual skulls were made with landmarks to track movements. An ideal treatment plan was created for each patient. Upper and lower boundaries for the dimensions of curvilinear distractors were established based on manufacturing and geometric constraints. Then, anatomically acceptable distractor attachment points were identified on the models using proximal and distal grids. Treatment plans were simulated for a series of distractors with varying radii of curvature, elongations (arc-length of device), and placements along the grids. The outcomes using these distractors were compared with the ideal treatment plans. Discrepancies were quantified in millimeters by comparing landmarks in the simulated versus ideal movements. RESULTS: Approximately 400,000 simulated 3-dimensional movements, based on the distractor parameters and variations in placement were computationally evaluated for the 18 cases. It was determined that, by varying distractor placement, a family of 5 distractors, with 3, 5, 7, and 10 cm radii of curvature and a straight-line device, could be used to treat all 18 cases to within 1.8 mm of error. CONCLUSIONS: The results of this study indicate that a family of 5 curvilinear distractors may suffice to treat a broad range of mandibular deformities.

Publication: Clin Anat. 2006 Jan;19(1):32-6. PMID: 16283638 | PDF

Authors: Li XP, Han DM, Xia Y, Zhou GH

Institution: Beijing Tongren Hospital Affiliated with Capital University of Medical Sciences, ENT Department, People's Republic of China.

Background/Purpose: The purpose of this study was to explore a feasible method for the reconstruction of the nasal and temporal bone structures of the Chinese virtual human project and provide a more accurate and facilitated way view them three-dimensionally (3D). The 3D Slicer software was used to reconstruct the anatomic structures of the human nose and temporal bone. Segmentation and extraction of the contours of the ROI (region of interest) in each single slice were conducted and the processed volume data was transferred into the 3D Slicer. After resegmentation, a set of labeled maps of the ROI were produced. Based on these maps, the 3D surface models of the tissues of interest were constructed. Four groups of paranasal sinuses, nasal septa, middle and inferior turbinates, temporal bones, tympanic cavities, mastoid air cells, sigmoid sinuses, and internal carotid arteries were reconstructed successfully. These models show spatial relationships and orientation between them. The results show that the 3D Slicer may be used for the 3D visualization of parts of anatomic structures in the nose and temporal bone based on the first Chinese virtual human data, and thus, can facilitate the observation and understanding of the anatomic structures in this area.

Funding:

• Beijing Natural Science Fund; Grant number: 7031001.

Publication: Proceedings of the Royal Society B: Biological Sciences 2006; 273:2605-2610. | PDF

Authors: Todd C. Rae, Una Strand Viðarsdottir, Nathan Jeffery A. Theodore Steegmann Jr

Institution: Evolutionary Anthropology Research Group, Department of Anthropology, University of Durham, 43 Old Elvet, Durham DH1 3HN, UK

Background/Purpose: Adaptation to climate occupies a central position in biological anthropology. The demonstrable relationship between temperature and morphology in extant primates (including humans) forms the basis of the interpretation of the Pleistocene hominin Homo neanderthalensis as a cold-adapted species. There are contradictory signals, however, in the pattern of primate craniofacial changes associated with climatic conditions. To determine the direction and extent of craniofacial change associated with temperature, and to understand the proximate mechanisms underlying cold adaptations in vertebrates in general, dry crania rom previous experiments on cold- and warm-reared rats were investigated using computed tomography scanning and three-dimensional digitization of cranial landmarks. Aspects of internal and external cranial morphology were compared using standard statistical and geometric morphometric techniques. The results suggest that the developmental response to cold stress produces subtle but significant changes in facial shape, and a relative decrease in the volume of the maxillary sinuses (and nasal cavity), both of which are independent of the size of the skull or postcranium. These changes are consistent with comparative studies of temperate climate primates, but contradict previous interpretations of cranial morphology of Pleistocene Hominini.

Funding:

• None. Prof. Steegmann supplied the materials, and the time on the pQCT machine was graciously donated by Prof. Tim Skerry of the Royal Veterinary College, London.

Publication: Journal of Vertebrate Paleontology 2006; 26:1018-1020. | PDF

Authors: A. A. Farke, T. E. Williamson

Institution: Department of Anatomical Sciences, Stony Brook University, N.Y.

Background/Purpose: Ceratopsid (horned dinosaur) cranial material is relatively common in the Upper Cretaceous Naashoibito Member of the Kirtland Formation, San Juan Basin, New Mexico. However, the specimens are fragmentary, making identification problematic. Previously, it has been suggested that the Naashoibito specimens represent Torosaurus utahensis, a chasmosaurine taxon originally known from the North Horn Formation of Utah. This identification has been used to support a Lancian age for the Naashoibito Member and the Alamo Wash local fauna of the Kirtland Formation (e.g., Lehman, 1981; Lucas et al., 1987). Others (e.g., Lehman, 1990) have synonomized T. utahensis with Torosaurus latus, a taxon otherwise known only from the late Maastrichtian Lance and Hell Creek formations. Recent work has upheld the validity of T. utahensis (Sullivan et al., 2005). However, Sullivan and colleagues (2005) have also argued that no previously described ceratopsid specimens from the Naashoibito Member are identifiable beyond the level of Chasmosaurinae indeterminate and therefore are not useful for assessing biostratigraphic correlations and ceratopsid biogeography. Here we describe a partial chasmosaurine ceratopsid parietal from the Naashoibito Member of the Kirtland Formation. Although other fragmentary parietals have been recovered from this unit (e.g., Lehman, 1981; Lucas et al., 1987), the new specimen exhibits unusual morphology: an epoccipital element positioned along the midline. This feature has previously been reported only in Triceratops, a taxon not known from south of the Denver Basin. The occurrence of such a feature in a ceratopsid from New Mexico has implications for ceratopsian systematics and biogeography.

Funding:

• NSF EAR 0207750

Publication: Obstet Gynecol. 2005 Dec;106(6):1259-65. PMID: 16319250 | PDF

Authors: Hsu Y, Fenner DE, Weadock WJ, DeLancey JO

Institution: Pelvic Floor Research Group, Division of Gynecology, Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan 48109-0276, USA.

Background/Purpose: To use magnetic resonance images of living women and 3-dimensional modeling software to identify the component parts and characteristic features of the external anal sphincter (EAS) that have visible separation or varying origins and insertions. METHODS: Detailed structural analysis of anal sphincter anatomy was performed on 3 pelvic magnetic resonance imaging (MRI) data sets selected for image clarity from ongoing studies involving nulliparous women. The relationships of anal sphincter structures seen in axial, sagittal, and coronal planes were examined using the 3D Slicer 2.1b1 software program. The following were requirements for sphincter elements to be considered separate: 1) a clear and consistently visible separation or 2) a different origin or insertion. The characteristic features identified in this way were then evaluated in images from an additional 50 nulliparas for the frequency of feature visibility. RESULTS: There were 3 components of the EAS that met criteria as being "separate" structures. The main body (EAS-M) is separated from the subcutaneous external anal sphincter (SQ-EAS) by a clear division that could be observed in all (100%) of the MRI scans reviewed. The wing-shaped end (EAS-W) has fibers that do not cross the midline ventrally, but have lateral origins near the ischiopubic ramus. This EAS-W component was visible in 76% of the nulliparas reviewed. CONCLUSION: Three distinct external anal sphincter components can be identified by MRI in the majority of nulliparous women.

Funding:

• P50 HD4406
• R01 HD38665

Publication: J Biomed Inform. 2005 Dec;38(6):431-42. PMID: 16337568 | PDF

Authors: Simmross-Wattenberg F, Carranza-Herrezuelo N, Palacios-Camarero C, Casaseca-de-la-Higuera P, Martin-Fernandez MA, Aja-Fernandez S, Ruiz-Alzola J, Westin CF, Alberola-Lopez C

Institution: Laboratorio de Procesado de Imagen, ETSI Telecomunicacion, Universidad de Valladolid, 47011 Valladolid, Spain

Background/Purpose: In this paper, we describe a first step towards a collaborative extension of the well-known 3D Slicer; this platform is nowadays used as a standalone tool for both surgical planning and medical intervention. We show how this tool can be easily modified to make it collaborative so that it may constitute an integrated environment for expertise exchange as well as a useful tool for academic purposes.

Funding:

• Comision Interministerial de Ciencia y Tecnologıa for Research Grant TIC2001-3808-C02
• NIH P41-RR13218
• CIMIT
• Network of Excellence SIMILAR FP6-507609

Publication: Enformatika Transactions on Engineering, Computing and Technology, November 2005; 9:157-161. | PDF

Author: Panos D. Kotsas

Institution: Department of Automated Control and System Engineering, University of Sheffield, UK.

Background/Purpose: This research deals with the application of a signal intensity independent registration criterion for 2D rigid body registration of medical images using 1D binary projections. The criterion is defined as the weighted ratio of two projections. The ratio is computed on a pixel per pixel basis and weighting is performed by setting the ratios between one and zero pixels to a standard high value. The mean squared value of the weighted ratio is computed over the union of the one areas of the two projections and it is minimized using the Chebyshev polynomial approximation using n=5 points. The sum of x and y parallel projections is used for translational adjustment and a range of parallel projections between 40-50 deg (depending on the orientation of the image) for rotational adjustment. MR-MR registration experiments were performed and gave mean errors well below 1deg and 1 pixel (0.12 deg and 0.47 pixels for the example given in Enformatika Publication). The method is to be extended for surface matching.

Publication: Neuroradiology. 2005 Jun;47(6):417-24. PMID: 15856213 | PDF

Authors: Strik HM, Borchert H, Fels C, Knauth M, Rienhoff O, Bähr M, Verhey JF.

Institution: Department of Neurology, Medical School, University of Göttingen, Germany.

Background/Purpose: Intracerebral haemorrhage still causes considerable disability and mortality. The studies on conservative and operative management are inconclusive, probably due to inexact volumetry of the haemorrhage. We investigated whether three-dimensional (3D), voxel-based volumetry of the haemorrhage and its mass effect is feasible with routine computed tomography (CT) scans. The volumes of the haemorrhage, ventricles, midline shift, the intracranial volume and ventricular compression in CT scans of 12 patients with basal ganglia haemorrhage were determined with the 3D Slicer software. Indices of haemorrhage and intracranial or ventricular volume were calculated and correlated with the clinical data. The intended measures could be determined with an acceptable intra-individual variability. The 3D volumetric data tended to correlate better with the clinical course than the conventionally assessed distance of midline shift and volume of haemorrhage. 3D volumetry of intracranial haemorrhage and its mass effect is feasible with routine CT examination. Prospective studies should assess its value for clinical studies on intracranial space-occupying diseases.

Publication: Obstet Gynecol. 2005 May;105(5 Pt 1):1012-7. PMID: 15863538 | PDF

Authors: Hsu Y, Chen L, Delancey JO, Ashton-Miller JA

Institution: Division of Gynecology, Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Background/Purpose: Use axial magnetic resonance imaging to test the null hypothesis that no difference exists in apparent vaginal thickness between women with and those without prolapse. METHODS: Magnetic resonance imaging studies of 24 patients with prolapse at least 2 cm beyond the introitus were selected from an ongoing study comparing women with prolapse with normal control subjects. The magnetic resonance scans of 24 women with prolapse (cases) and 24 women without prolapse (controls) were selected from those of women of similar age, race, and parity. The magnetic resonance files were imported into an experimental modeling program, and 3-dimensional models of each vagina were created. The minimum transverse plane cross-sectional area, mid-sagittal plane diameter, and transverse plane perimeter of each vaginal model were calculated. RESULTS: Neither the mean age (cases 58.6 years ± standard deviation [SD] 14.4 versus controls 59.4 years ± SD 13.2) nor the mean body mass index (cases 24.1 kg/m²± SD 3.3, controls 25.7 kg/m²± SD 3.7) differed significantly between groups. Minimum mid-sagittal vaginal diameters did not differ between groups. Patients with prolapse had larger minimum vaginal cross-sectional areas than controls (5.71 cm²± standard error of the mean [SEM] 0.25 versus 4.76 cm²± SEM 0.20, respectively; P = .005). The perimeter of the vagina was also larger in the prolapse group (11.10 cm ± SEM 0.24) compared with controls (9.96 cm ± SEM 0.22) P = .001. Subgroup analysis of patients with endogenous or exogenous estrogen showed prolapse patients had larger vaginal cross-sectional area (P = .030); in patients without estrogen group differences were not significant (P = .099). CONCLUSION: Vaginal thickness is similar in women with and those without pelvic organ prolapse. The vaginal perimeter and cross-sectional areas are 11% and 20% larger in prolapse patients, respectively. Estrogen status did not affect differences found between groups.

Funding:

• NIH R01 HD038665

Publication: J Comput Assist Tomogr. 2005 May-Jun;29(3):305-10. PMID: 15891495 | PDF

Authors: Bartling S, Peldschus K, Rodt T, Kral F, Matthies H, Kikinis R, Becker H.

Institution: Department of Neuroradiology, Hannover Medical School, Hannover, Germany.

Background/Purpose: CT and MRI of the skull base and the Temporal provides complimentary information. A registration and fusion of CT and MRI may improve diagnosis, because features only seen in one modality can be assessed with respect to the information gathered from the other modality. A manual, rigid registration method - basically overlaying two volumes in one space - as implemented in 3D Slicer was used. Threshold based fusion methods resulted in MRI overlaying co-registered CT. Landmarks have been used to assess target registration error - registration accuracy was within the range of the voxel size of either modality. A range of different pathological conditions was used to demonstrate the potential benefits of this methods.

Publication: Breast Cancer. 2005;12(1):26-31. PMID: 15657520 | PDF

Authors: Abe H, Kurumi Y,Naka S, Shiomi H, Umeda T, Naitoh H, Endo Y, Hanasawa K, Morikawa S, Tani T.

Institution: Division of General Surgery, Department of Surgery, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan.

Background/Purpose: Liver metastases from breast cancer are associated with a poor prognosis, however, local control with microwave thermocoagulation therapy has been used in certain subgroups of these patients in the past decade. In this study, open-configuration magnetic resonance (MR) -guided microwave thermocoagulation therapy was used for metastatic liver tumors from breast cancer, and the efficacy of this treatment was assessed. METHODS: Between June 2000 and April 2004, we used MR-guided microwave thermocoagulation therapy on 11 nodules in 8 patients with metastatic liver tumors from breast cancer. The procedure was carried out under general anesthesia. A 0.5 T open-configuration MR system and a microwave coagulator were used. Near-real-time MR images and real-time temperature images were collected and displayed on the monitor. The MR-compatible thoracoscope was used and combined with MR imaging guidance. Navigation software, a 3D Slicer, was installed and customized. RESULTS: The customized navigation software displayed near-real-time MR images. The percutaneous puncture into the tumors was successful in all cases. No mortality or major complications occurred as a result of the procedures. Five of the 8 patients are alive with new metastatic foci with a mean observation period of 25.9 months. CONCLUSIONS: We developed several devices to allow safe, easy, and accurate MR-guided microwave thermocoagulation therapy of liver tumors. Open-configuration MR-guided microwave thermocoagulation therapy appears to be a feasible method for tumor ablation of metastatic liver tumors from breast cancer.

Publication: Magn Reson Med. 2005 Feb;53(2):474-8. PMID: 15678546 | PDF

Authors: Tina A. Lewis, Yang-Sheng Tzeng, Erin L. McKinstry, Angela C. Tooker, Kwansoo Hong, Yanping Sun, Joey Mansour, Zachary Handler, and Mitchell S. Albert

Institution: Brigham and Womem's Hospital, Harvard Medical School, Boston, MA, USA.

Background/Purpose: As another step toward extracting quantitative information from hyperpolarized 3He MRI, airway diameters in humans were measured from projection images and multislice images of the lungs. Values obtained were in good agreement with the Weibel lung morphometry model. The measurement of airway caliber can now be achieved without the use of ionizing radiation. Furthermore, it was demonstrated that 3D airway tree renderings could be constructed from the multislice data. Both the measurement of airway diameters and the rendering of 3D airway information hold promise for the clinical assessment of bronchoconstrictive diseases such as asthma and the associated evaluation of treatment effectiveness. Work is being done to address the uncertainties of the manually intensive methods we have developed.

Funding:

• R21-EB1689/EB/NIBIB NIH HHS/United States
• R33 EB001689-02/EB/NIBIB NIH HHS/United States

Publication: Ann. N.Y. Acad. Sci. 2005; 1064:134–148. PMID: 16394153 | PDF

Authors: Marek Kubicki, Carl-Fredrik Westin, Robert W. McCarley, and Martha E. Shenton

Institution: Clinical Neuroscience Division, Laboratory of Neuroscience, Boston VA Healthcare System–Brockton Division, Department of Psychiatry, Harvard Medical School, Brockton, Massachusetts, USA

Background/Purpose: Schizophrenia is a serious and disabling mental disorder that affects approximately 1% of the general population, with often devastating effects on the psychological and financial resources of the patient, family, and larger community. The etiology of schizophrenia is not known, although it likely involves several interacting biological and environmental factors that predispose an individual to schizophrenia. However, although the underlying pathology remains unknown, it has been believed that brain abnormalities would ultimately be linked to the etiology of schizophrenia. This theory was rekindled in the 1970s, when the first computer-assisted tomography (CT) study showed enlarged lateral ventricles in schizophrenia. Since that time, there have been many improvements in MR acquisition and image processing, including the introduction of positron emission tomography (PET), followed by functional MR (fMRI), and diffusion tensor imaging (DTI). These advances have led to an appreciation of the critical role that brain abnormalities play in schizophrenia. While structural MRI has proven to be useful in investigating and detecting gray matter abnormalities in schizophrenia, the investigation of white matter has proven to be more challenging as white matter appears homogeneous on conventional MRI and the fibers connecting different brain regions cannot be appreciated. With the development of DTI, we are now able to investigate white matter abnormalities in schizophrenia.

Funding:

• NIH R03 MH 068464-02
• NIH R01 NS 39335
• NIH R01 MH 40799
• NIH K02 MH 01110
• NIH R01 MH 50747

Publication: Proceedings of the 2004 IEEE International Conference on Robotics & Automation, ICRA 2004.|PDF

Authors: Ming Li, Russell H. Taylor

Institution: Department of Computer Science, NSF Engineering Research Center for Computer Integrated Surgical Systems and Technology, Johns Hopkins University, Baltimore, MD, USA.

Background/Purpose: In Ear, Nose and Throat (ENT) surgery, the operating volume is very limited. This is especially true in sinus surgery, when the instrument passes through the nasal and sinus cavity to reach the pathological area. The nasal and sinus bones impose geometric constraints on the work volume. During the surgery, the surgeon needs to control the motion of the instrument tip to accomplish some delicate procedure; meanwhile he/she needs to avoid hitting anatomic constraints. In this paper, we present a method to assist the path following task in a constrained area. The system reads the user’s force input and combines it with the planned tip-trajectory to create the tip motion constraints; meanwhile it generates the tool-shaft boundary constraints based on a 3D geometric model. We map instrument tip motion and boundary information to joint displacements via robot kinematics, and then use a constrained quadratic optimization algorithm to compute the optimal set of corresponding joint displacements. In the preliminary study, we show that robot guidance using cooperative control and virtual fixtures derived from complex geometry can assist users in skilled manipulation tasks, while maintaining desirable properties such as collision avoidance and safety.

Funding:

• National Science Foundation under grants EEC9731748, IIS9801684, IIS0099770, IIS0205318

Publication: J Appl Clin Med Phys. 2004 Summer;5(3):66-79. PMID: 15753941 | PDF

Authors: Veninga T, Huisman H, van der Maazen RW, Huizenga H.

Institution: Department of Radiation Oncology, University Medical Center Nijmegen, The Netherlands.

Background/Purpose: Image registration integrates information of different imaging modalities and has the potential to improve target volume determination in radiotherapy planning. This paper describes the implementation and validation of a 3D fully automated registration procedure in the process of radiotherapy treatment planning of brain tumors. 15 Patients with various brain tumors received CT and MR brain imaging before the start of radiotherapy. The normalized mutual information (NMI) method was used for image registration. Registration accuracy was estimated by performing statistical analysis of coordinate differences between CT and MR anatomical landmarks along the x-, y- and z-axes. Second, a visual validation protocol was developed to validate the quality of individual registration solutions and this protocol was tested in a series of 36 CT-MR registration procedures with intentionally applied registration errors. The mean coordinate differences between CT and MR landmarks along the x- and y-axes were in general within 0.5 mm. The mean coordinate differences along the z-axis were within 1.0 mm, which is of the same magnitude as the applied slice thickness in scanning. Second, the detection of intentionally applied registration errors by employment of a standardized visual validation protocol resulted in low false-negative and low false-positive rates. Application of the NMI method for the brain results in excellent automatic registration accuracy and the method has been incorporated in daily routine within our institute. A standardized validation protocol is proposed that ensures the quality of individual registrations by detecting registration errors with high sensitivity and specificity. This protocol is proposed for the validation of other linear registration methods.

Publication: J Neurosurg. 2004 Jul;101(1):66-72. PMID: 15255253 | PDF

Authors: Berman JI, Berger MS, Mukherjee P, Henry RG.

Institution: Department of Radiology, University of California at San Francisco, CA, USA.

Background/Purpose: The goal of this study was to use diffusion-tensor (DT) magnetic resonance (MR) imaging to track fibers com- bined with cortical stimulation mapping to delineate descending motor pathways. Subcortical localization of motor path-ways in relation to a glioma may provide critical information to guide tumor resection and prevent surgical morbidity. Methods. Eleven adult patients harboring gliomas underwent MR imaging 1 day prior to image-guided intraoperative cortical motor mapping and tumor resection. Screens depicting 27 cortical motor sites on a surgical navigation system were saved to launch DT imaging of fiber tracks of descending motor pathways. The position and organization of motor tracts were visualized by fiber tracking. Tracks from 16 motor stimulation sites followed descending pathways from the precentral gyrus, through the corona radiata and internal capsule, and into the cerebral peduncle. These tracks were also observed on DT images to diverge along crossing white matter bundles (four patients) and to terminate or deviate in regions of peritumoral vasogenic edema (five patients). Conclusions. The use of precise intraoperative cortical mapping information and DT images of fiber tracks can reveal the course of motor pathways beneath the cortex. The subcortical fiber tracks generated are consistent with the known anatomical course and somatotopic organization of the motor tract in relation to its cortical origins. Tracking fibers by using DT imaging in combination with functional localization has the potential to reduce surgical morbidity by revealing subcortical connections of the functional cortex.

Funding:

• NIH K01CA76998

Publication: NeuroImage 2004; 22:720–727. PMID: 15193600 | PDF

Authors: Hidenori Yamasue, Haruyasu Yamada, Masato Yumoto, Satoru Kamio, Noriko Kudo, Miki Uetsuki, Osamu Abe, Rin Fukuda, Shigeki Aoki, Kuni Ohtomo, Akira Iwanami Nobumasa Kato, Kiyoto Kasai

Institution: Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Bunkyo, Tokyo 113-8655, Japan

Background/Purpose: Schizophrenia is associated with language-related dysfunction. A previous study [Schizophr. Res. 59 (2003c) 159] has shown that this abnormality is present at the level of automatic discrimination of change in speech sounds, as revealed by magnetoencephalographic recording of auditory mismatch field in response to across-category change in vowels. Here, we investigated the neuroanatomical substrate for this physiological abnormality. Thirteen patients with schizophrenia and 19 matched control subjects were examined using magnetoencephalography (MEG) and high-resolution magnetic resonance imaging (MRI) to evaluate both mismatch field strengths in response to change between vowel /a/ and /o/, and gray matter volumes of Heschl's gyrus (HG) and planum temporale (PT). The magnetic global field power of mismatch response to change in phonemes showed a bilateral reduction in patients with schizophrenia. The gray matter volume of left planum temporale, but not right planum temporale or bilateral Heschl's gyrus, was significantly smaller in patients with schizophrenia compared with that in control subjects. Furthermore, the phonetic mismatch strength in the left hemisphere was significantly correlated with left planum temporale gray matter volume in patients with schizophrenia only. These results suggest that structural abnormalities of the planum temporale may underlie the functional abnormalities of fundamental language-related processing in schizophrenia.

Funding:

• C12670928 Ministry of Education, Culture, Sport, Science and Technology, Japan
• Welfide Medicinal Research Fundation, Japan
• Uehara Memorial Fundation, Japan

Publication: Acad Radiol. 2003 Dec;10(12):1442-9. PMID: 14697012 | PDF

Authors: Morikawa S, Inubushi T, Kurumi Y, Naka S, Sato K, Demura K, Tani T, Haque HA, Tokuda J, Hata N.

Institution: Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Ohtsu, Shiga 520-2192, Japan.

Background/Purpose: The purpose of this study was to utilize computer assistance effectively for both easy and accurate magnetic resonance (MR) image-guided microwave thermocoagulation therapy of liver tumors. MATERIALS AND METHODS: An open configuration MR scanner and a microwave coagulator at 2.45 GHz were used. Navigation software, a 3D Slicer, was customized to combine fluoroscopic MR images and preoperative MR images for the navigation. New functions to display MR temperature maps with simple parameter setting, and to record and display the coagulated areas by multiple microwave ablations in the 3-dimensional space (footprinting), were also introduced into the software. The VGA signal of the computer display was directly transferred to the surgeon's monitor. RESULTS: The customized software could be used for both accurate image navigation and convenient and easy temperature monitoring. Because repeated punctures and ablations are usually required in this procedure, the footprinting function made targeting of the tumors both easy and accurate and was quite effective in achieving the necessary and sufficient treatment. Furthermore, clear display on the surgeon's monitor, which was obtained by direct transfer of the VGA signal, enabled precise image navigation. CONCLUSION: The newly developed computer assistance was quite useful and helpful for this MR-guided procedure.

Publication: Osteoarthritis Cartilage. 2003 Oct;11(10):725-9. PMID: 13129691 | PDF

Authors: Hunter DJ, March L, Sambrook PN.

Institution: Institute of Bone and Joint Research, Royal North Shore Hospital, Sydney, Australia.

Background/Purpose: Whilst the characteristic pathologic feature of OA is the loss of hyaline cartilage, prior studies have demonstrated a poor relationship between severity of reported knee pain and degree of radiographic change. The aim of this study was to examine the association between knee symptoms and MRI cartilage volume. DESIGN: A cross-sectional study was performed to assess the association between knee symptoms and MRI cartilage volume in an unselected, community based population. The subjects were 133 postmenopausal females. The subjects had a T2-weighted fat saturated sagittal gradient-echo MRI performed of their right knee. Femoral, tibial and patella cartilage volumes were measured using three-dimensional 3D Slicer, a software that facilitates semi-automatic segmentation, generation of 3D surface models and quantitative analysis. Qualitative data relating to symptoms, stiffness, pain, physical dysfunction and the quality of life using the WOMAC were recorded. The statistical analyses conducted to determine measures of association between knee pain/symptoms and cartilage volume were correlation, multiple regression and inter-quartile regression. RESULTS: Assessment of the association between patella cartilage volume and the WOMAC domains showed an inverse relationship between patella cartilage volume and pain, function and global score in a model including body mass index, physical activity and leg extensor power (all P=0.01). Inter-quartile regression comparing the lowest 25% with highest 25% patella cartilage volume demonstrated a stronger inverse relationship (P=0.005). CONCLUSION: This study suggests that alterations in patella volume are associated with pain, function and global scores of the WOMAC. In participants with more knee pain, there was an association with severity of patella cartilage reduction. Other MRI cartilage volume features were not strongly associated with WOMAC sub-scores.

Publication: Am J Obstet Gynecol. 2003 Jul;189(1):130-5. PMID: 12861151 | PDF

Authors: Cornella JL, Hibner M, Fenner DE, Kriegshauser JS, Hentz J, Magrina JF.

Institution: Mayo Graduate School of Medicine, USA.

Background/Purpose: The purpose of this study was to assess the correlation between internal and external anal sphincter volumes and manometric anal pressures. STUDY DESIGN: Ten healthy nulliparous women underwent anal sphincter magnetic resonance imaging and anal manometry measurement. A 3-dimensional reconstruction of magnetic resonance images was accomplished with the use of 3D Slicer. Sphincter volumes were measured 3 times by the same observer for each of 10 patients. The intrarater reliability was measured with the use of the intraclass correlation coefficient (ICC = sigma²(patients)/(sigma ²(patients) + sigma²(error))) from a 2-way analysis of variance model with terms for patient and measurement trial. Measurements that were recorded on anal manometry included squeeze length, length of the high-pressure zone, and maximal resting and squeeze pressures. RESULTS: The mean volumes (± SD) were 18.77 ± 4.64 cm³, 13.82 ± 3.8 cm³, and 32.36 ± 8.37 cm³ for internal, external, and combined sphincters, respectively. Intrarater reliability was 98% for external sphincter volume (95% CI, 94%-99%), 98% for internal sphincter volume (95% CI, 94%-99%), and 99% for total volume (95% CI, 97%-100%). On the 3-dimensional images, the internal sphincter was found to be cylindric in shape, with an ellipse as a base. It is elongated in the anterior and posterior direction and flattened on the sides. The external sphincter was found to be funnel-shaped, being narrower caudad and widening in the cephalad direction. Similar to the internal sphincter, the external sphincter is elongated in the anteroposterior diameter. Volumes of the internal, external, and combined sphincters did not correlate with the maximum pressures at rest and squeeze. Correlations higher than r = 0.5 were observed for all 3 sphincter volume measurements versus high pressure zone at squeeze. The highest correlation, r = 0.66, was for internal sphincter volume versus high pressure zone at squeeze CONCLUSION: Three-dimensional reconstruction of the rectal sphincter musculature can be performed easily with 3-dimensional software. Measurements of the sphincter volumes have excellent intrarater reliability. Sphincter volumes do not correlate with pressures at rest or squeeze, but the internal sphincter volume correlates with the length of the high pressure zone at squeeze. Contrary to current generalized concepts, it is possible that the internal sphincter may play some role in generating the squeeze pressure. More research is necessary in applying 3-dimensional magnetic resonance image reconstruction in patients with different parity and continence status. Reconstruction of magnetic resonance images of the rectal sphincter musculature may prove to be beneficial in planning the treatment of patients with fecal incontinence.

Publication: Rheumatology (Oxford). 2003 Dec;42(12):1495-500. PMID: 12832711 | PDF

Authors: David J. Hunter, Harold Snieder, Lyn March, and Philip N. Sambrook

Institution: Institute of Bone and Joint Research, Royal North Shore Hospital, University of Sydney, Australia.

Background/Purpose: A classical twin study was performed to assess the relative contribution of genetic and environmental factors to cartilage volume. METHODS: The subjects were 136 adult female twins: 31 monozygotic and 37 dizygotic twin pairs. The subjects had a T2-weighted fat-saturated sagittal gradient echo MRI performed of their right knee. Femoral, tibial and patella cartilage volumes were measured using 3D Slicer, a piece of software that facilitates semi-automatic segmentation, generation of three-dimensional surface models and quantitative analysis. The intraclass correlations were calculated, and maximum-likelihood model fitting was used to estimate genetic and environmental variance components. All variables were adjusted for age, BMI and femoral condyle size. RESULTS: The intraclass correlations for all of the cartilage volumes assessed were higher in monozygotic than dizygotic twin pairs. The heritabilities (95% confidence intervals) obtained from model fitting were: femoral, 61% (36-77%); tibial, 76% (56-87%); patella, 66% (47-79%); and total cartilage volume, 73% (51-85%). CONCLUSION: This study provides evidence for the importance of genetic factors in determining cartilage volume. Identifying heritability is the first step on the way to finding specific genes, which may improve our insight in the pathophysiology of cartilage disorders including the etiology of complex diseases such as osteoarthritis.

Funding:

• Ramsay Health Care Fellowship and the Royal Australasian College of Physicians.

Publication: Stud Health Technol Inform. 2003;94:65-71. PMID: 15455866 | PDF

Authors: Enciso R, Memon A, Fidaleo DA, Neumann U, Mah J.

Institution: Craniofacial Virtual Reality Laboratory, University of Southern California, CA, USA.

Background/Purpose:Recent developments in technology and software are providing better data and methods to facilitate research in biomedical modeling and simulation. In the area of segmentation, original methods involved the time-consuming task of manually tracing structures from slice to slice. This process is now possible with significantly less interaction from the user. Programs such as 3D Slicer [6], Mimics (Materialise N.V., Heverlee, Belgium) and Amira 2.3 (TGS) provide semi-automatic image-processing-based segmentation and modeling from CT images. These programs use the Generalized Marching Cubes algorithm to create a polygonal wireframe mesh of the segmented area and export a model in STL or other formats.

Funding:

• NSF EEC-9529152