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3D Slicer Enabled Research

3D Slicer is a free open source software package distributed under a BSD style license. The majority of funding for the development of 3D slicer comes from a number of grants and contracts from the National Institutes of Health (see Slicer Acknowledgments for more information).

We invite you to provide information on how you are using 3D Slicer to produce peer-reviewed research. Information about the scientific impact of this tool is helpful in raising funding for the continued support of this tool.


Contrast-maximizing adaptive region growing for CT

File:Airways.png
Airway segmentation.
Muscle segmentation.

Publication: Poster Presentation at the Second International Workshop on Pulmonary Image Analysis. Poster PDF, Paper PDF. Oral Presentation at ACIVS 2009. Paper PDF.

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. Results have been obtained in the context of surgical planning (bone, muscle and fat segmentation) and pulmonary image analysis (airway segmentation).

New EMSegment Module in Slicer3

New EMSegment Module in Slicer3. We improved the usability of EMSegment in a clinical setting and studied the influence of MRI Bias Field Correction on the segmentation accuracy.

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

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

Institution: 1 ISEN Brest (France), 2 MIT CSAIL, 3 Harvard 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.

Computer-aided 3D visualization in oto-rhino-laryngology

Maxilloethmoidal tumor. Red: tumor; orange: cranium (and some other soft tissues); green: eyeball; blue: eye muscles; yellow: optical nerve

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.

Morphology, constraints, and scaling of frontal sinuses in the hartebeest, Alcelaphus buselaphus (Mammalia: Artiodactlya, Bovidae)

Farke-Morphology2007-fig-mj.jpg

Publication: Journal of Morphology 2007; 268:243-253. 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.

How volumetric analysis quantifies therapeutic response of slow-flow vascular malformations

A 5-year-old boy with a large slow-flow malformation of the upper lip and left midface before (left) and after (right) 6 sessions of percutaneous sclerotherapy and final surgical resection at his 6th birthday.

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.

A computer modelling tool for comparing novel ICD electrode orientations in children and adults

Figure 7: Patient-specific modeling in a patient with congenital heart disease.

Publication: Heart Rhythm. 2008 Apr;5(4):565-572. 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.

Grant Support:

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

Towards scarless surgery: An endoscopic ultrasound navigation system for transgastric access procedures

Figure 3: View of the system interface as presented to the clinician.

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

Grant Support:

  • NIH P41-RR13218
  • CIMIT

Image-guided Otologic Surgery based on Patient Motion Compensation and Intraoperative Virtual CT

Red object represents internal carotid artery, and the green represents a cyst. The surgeon must open the cyst avoiding injury into the artery.

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.

Non-rigid registration of pre-procedural MR images with intra- procedural unenhanced CT images for improved targeting of tumors during liver radiofrequency ablations

Figure 3: The position of RF applicator and tumor margin are illustrated on both axial images. Advanced 3D visualization using 3D Slicer enables accurate estimation of RFA electrode with respect to the tumor margins.

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

Grant Support:

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

Using 3D Slicer in Astronomy

Astromed1-mj.jpg

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.

Origin and insertion points involved in levator ani muscle defects

Figure 2: Three-dimensional model of the pelvis.

Publication: Am J Obstet Gynecol. 2007 Mar;196(3):251.e1-5. 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 three-dimensional 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.

Grant Support:

  • 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.

Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer

Left: The diagram displays the sub-cellular EGFR gene-protein interaction network that combines nucleus, cytoplasm and membrane compartments. Right: 3D snapshot of the tumor system.

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

Grant Support:

  • NIH CA 085139
  • NIH CA 113004

Image Registered FAST (IRFAST) for Combat Casualty Triage

Automatic segmentation of a CT scan. The image was produces by a method developed by Dr. Pohl, where the label map of previously analyzed CT scan guides the segmentation of the CT scan of this subject.

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.

Grant Support: This work partially supported by SBIR SNC06C0003 TATRC/CIMIT for Image Guided FAST Ultrasound.

A Preliminary Study on the Relationship between Nasal Cavity and Maxillary Sinus Volumes

Color labels of segmented areas were then rendered using the “Model Module” in 3D Slicer to create 3-D models. Using the “MeasVol Module,” absolute volumes of the nasal cavity and each maxillary sinus were quantified.

Publication: roceedings 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.

Registered, Sensor-Integrated Virtual Reality for Surgical Applications

Figure 2: Visualization System

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.

Modeling Cancer Biology

From Patients to Molecules and Back. MRI images from a brain tumor patient (left) are used to build a 3-D in silico model of the growing tumor (right).

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

Author: Kristin Cobb

Interventional navigation for abdominal surgery by simultaneous use of MRI and ultrasound

Bright blue object represents a cyst, and the red represents a part of portal vein. The green is a target tumor. The physician must insert a needle into the tumor avoiding the vessel and cyst.

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

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.

A Comparison of Upper Airway Structures in Male and Female Obstructive Sleep Apnoea (OSA) Patients

Poster Presentation at the 2007 American Thoracic Society International Conference.

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: www.slicer.org) 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.

Grant Support:

  • Royal Australian and New Zealand College of Radiologists

A 3D Model Simulating Sediment Transport, Erosion and Deposition within a Network of Channel Belts and an Associated Floodplain

Karssenberg1.png

Publication: PowerPoint Presentation PDF

Authors: Derek Karssenberg and John Bridge

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

Molecular Diffusion in MRI: Technical Application of Fiber Tracking

Mora.png

Publication: PowerPoint Presentation PPT

Author: Martha Liliana Mora V.

Institution: Rey Juan Carlos University, Madrid, Spain.

Quantification of Levator Ani Cross-sectional Area Differences between Women with and those without Prolapse

Figure 2: 3D Slicer models. A. Three-fourths view of the levator ani muscle and pubic bone. B. Levator ani with pubic bones removed. C. Lateral view of muscle.

Publication: Obstet Gynecol. 2006 Oct;108(4):879-83. 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.

Grant Support:

  • NIH R01 HD-38665
  • DGF HU1502

Liver metastases: 3D shape-based analysis of CT scans for detection of local recurrence after radiofrequency ablation

Figure 2: Follow-up CT scans obtained 9 and 12 months after RF ablation. Three-dimensional views of tumor on reference transverse plane show results of ablated tumor segmentations. Three-dimensional shape changes related to recurrence are seen at months 9 and 12 (arrows).

Publication: Radiology. 2006 Oct;241(1):243-50. 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.

Grant Support:

  • Study grant from the French Radiological Society

Atlas Guided Identification of Brain Structures by Combining 3D Segmentation and SVM Classification

Figure 2: WM and GM identification. The upper row presents classification results projected on a 2D T1 slice. The lower row demonstrates a 3D view of the results. a. WM-Ground-Truth b. WM-Automatic c. GM-Ground-Truth d. GM-Automatic

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

Grant Support:

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

Development of a CAD (Computer Assisted Detection) System to Detect Lung Nodules in CT Scans

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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).

Dynamic Simulation of Joints Using Multi-Scale Modeling

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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.

Grant Support:

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

Quasi-isometric Flattening of Curved Surfaces for Medical Imaging

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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 .

Grant Support:

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

A Translation Station for Imaging

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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.

Habitual Use of the Primate Forelimb is Reflected in the Material Properties of Subchondral Bone in the Distal Radius

Figure 2: Maximum intensity projection (MIP) maps for radii superimposed upon 3D virtual reconstructions of the same distal radii.

Publication: J Anat. 2006 Jun; 208(6):659-670. 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.

Grant Support: Funding for this research was provided by Sigma Xi Grants-In-Aid of Research to B.A.P.

Appearance of the Levator Ani Muscle Subdivisions in Magnetic Resonance Images

Figure 1: A. Three-dimensional model of levator ani subdivisions including the pubic bone and pelvic viscera. B. The same model without the pubic bone.

Publication: Obstet Gynecol. 2006 May;107(5):1064-9. 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.

Grant Support:

  • NICHD P50 HD 44406
  • R01 HD 38665

Virtual Cystoscopy - A Surgical Planning and Guidance Tool

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

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.

Measurement of the Pubic Portion of the Levator ani Muscle in Women with Unilateral Defects in 3D Models from MR Images

Figure 2: (A) Reconstructed 3-D model showing the pubic bone and levator ani muscle with a right unilateral defect. (B) The dashed region shows the expected location of the missing muscle after reflecting the muscle from the normal side across the midline.

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

Grant Support:

  • NICHD R01 HD-38665

Range of Curvilinear Distraction Devices Required for Treatment of Mandibular Deformities

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

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.

Preliminary Study on Digitized Nasal and Temporal Bone Anatomy

Figure 3: Internal view of reconstructed right temporal bone and paranasal sinuses. 1, frontal sinus; 2, ethmoid sinus; 3, maxillary sinus; 4, sphenoid sinus; 5, orbit; 6, temporal bone.

Publication: Clin Anat. 2006 Jan;19(1):32-6. 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.

Grant Support:

  • Beijing Natural Science Fund; Grant number: 7031001.

Developmental Response to Cold Stress in Cranial Morphology of Rattus: Implications for the Interpretation of Climatic Adaptation in Fossil Hominins

Figure 1: Three-dimensional virtual reconstruction of rat cranium (norma superioralis) from pQCT scans. (a) A reconstruction of the external surface of the bone. (b) The same specimen with the bone made opaque and the maxillary sinuses highlighted in blue.

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.

Grant Support: 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.

A ceratopsid dinosaur parietal from New Mexico and its implications for ceratopsid biogeography and systematics

Figure 1: E. parietal reconstructed digitally without epoccipital. The epoccipital has been displaced directly caudally, to show its relationship to the caudal border of the parietal.

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.

Grant Support:

  • NSF EAR 0207750

Magnetic Resonance Imaging and 3-Dimensional Analysis of External Anal Sphincter Anatomy

Figure 1: A. Inferior, left three-quarter view of model showing relationship of external anal sphincter complex to the bones and pelvic organs. B. Inferior, left three-quarter view of the external anal sphincter complex. External anal sphincter is in red; note the lateral wing portion of the external anal sphincter. Subcutaneous external anal sphincter is in orange. C. Posterior view of the external anal sphincter complex showing the circumferential nature of both the external anal sphincter and the subcutaneous external anal sphincter. U, urethra; B, bladder; V, vagina; LA, levator ani muscle; R, Rectum; EAS-M, main body of external anal sphincter; EAS-W, lateral wing portion of the external anal sphincter; SQ-EAS, subcutaneous external anal sphincter.

Publication: Obstet Gynecol. 2005 Dec;106(6):1259-65. 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.

Grant Support:

  • P50 HD4406
  • R01 HD38665

Group-Slicer: a collaborative extension of 3D Slicer

Figure 7: A. A mouse click on the computer on the right. The user starts dragging a slider to move the cutting plane.

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

Grant Support:

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

2D Rigid Registration of MR Scans using the 1D Binary Projections

Figure 2: T2 MR scan (contrast enhanced) and mask created with 3D Slicer software

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.

Three-dimensional reconstruction and volumetry of intracranial haemorrhage and its mass effect

Figure 1: The process to identify the bleeding.

Publication: Neuroradiology. 2005 Jun;47(6):417-24. 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.

Vaginal Thickness, Cross-Sectional Area, and Perimeter in Women with and Those without Prolapse

Figure 1: Axial slices at 5-mm intervals arranged caudal to cephalad starting from the image in the upper left (image 0). Vaginal tracings were made from above the level of the vestibular bulbs (VB), represented by asterisks (*), caudally (image 0) to below where the cervix (C) could be seen (image -4.0). U, urethra; V, vagina; R, rectum; B, bladder.

Publication: Obstet Gynecol. 2005 May;105(5 Pt 1):1012-7. 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/m(2)± SD 3.3, controls 25.7 kg/m(2)± 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 cm(2)± standard error of the mean [SEM] 0.25 versus 4.76 cm(2)± 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.

Grant Support:

  • NIH R01 HD038665

Open-configuration MR-guided Microwave Thermocoagulation Therapy for Metastatic Liver Tumors from Breast Cancer

Publication: Breast Cancer. 2005;12(1):26-31.

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.

The Application of DTI to Investigate White Matter Abnormalities in Schizophrenia

Figure 6: Fibers traveling through the splenium of the corpus callosum are shown, where fibers connecting the left and right occipital lobe are displayed in green, fibers interconnecting lateral temporal regions are displayed in red, and fibers connecting medial temporal regions are displayed in blue. Additionally, the genu of the corpus callosum is labeled as “G”, the body as “B”, the isthmus as “I”, and the splenium as “S”.

Publication: Ann. N.Y. Acad. Sci. 2005; 1064:134–148. 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.

Grant Support:

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

Abnormal Association between Reduced Magnetic Mismatch Field to Speech Sounds and Smaller Left Planum Temporale Volume in Schizophrenia

Figure 1: (Panels A and B) Delineation of Heschl’s gyrus and planum temporale in a coronal slice in rostral and caudal part of regions of interest, respectively, based on MRI data of a control subject. The gray matter of Heschl’s gyrus is labeled green on subject left and wine-red on subject right. The gray matter of planum temporale is orange on subject left and violet on subject right. (C) Sagittal view of the Heschl’s gyrus and planum temporale in the left hemisphere. The coronal lines A and B correspond to the planes of panels A and B, respectively. (D) Three-dimensional reconstruction of Heschl’s gyrus and planum temporale gray matter superimposed on the axial plane. Each region is labeled using the same color as that in panels A, B and C.

Publication: NeuroImage 2004; 22:720–727. 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.

Grant Support:

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

Advanced computer assistance for magnetic resonance-guided microwave thermocoagulation of liver tumors

Morikawa-AcadRadiol2003-fig.png

Publication: Acad Radiol. 2003 Dec;10(12):1442-9.

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.

The association of cartilage volume with knee pain

Publication: Osteoarthritis Cartilage. 2003 Oct;11(10):725-9. 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.

Three-dimensional reconstruction of magnetic resonance images of the anal sphincter and correlation between sphincter volume and pressure

Figure 2: Axial view with outlined external (blue) and internal (red) sphincters. The anal canal is outlined (black) so that its volume can be subtracted from the volumes of internal and external sphincter.

Publication: Am J Obstet Gynecol. 2003 Jul;189(1):130-5. 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 3-dimensional 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 = sigma (2)(patients)/(sigma (2)(patients) + sigma (2)(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 cm(3), 13.82 ± 3.8 cm(3), and 32.36 ± 8.37 cm(3) 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.

Genetic contribution to cartilage volume in women: a classical twin study

Publication: Rheumatology 2003 42: 1495-1500. 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.

Grant Support:

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