Pohl KM, Fisher J, Kikinis R, Grimson EWL, Wells WM. Shape Based Segmentation of Anatomical Structures in Magnetic Resonance Images. Comput Vis Biomed Image Appl. 2005;3765 :489-98.Abstract
Standard image based segmentation approaches perform poorly when there is little or no contrast along boundaries of different regions. In such cases, segmentation is largely performed manually using prior knowledge of the shape and relative location of the underlying structures combined with partially discernible boundaries. We present an automated approach guided by covariant shape deformations of neighboring structures, which is an additional source of prior information. Captured by a shape atlas, these deformations are transformed into a statistical model using the logistic function. Structure boundaries, anatomical labels, and image inhomogeneities are estimated simultaneously within an Expectation-Maximization formulation of the maximum a posteriori probability estimation problem. We demonstrate the approach on 20 brain magnetic resonance images showing superior performance, particularly in cases where purely image based methods fail.
Warfield SK, Haker SJ, Talos I-F, Kemper CA, Weisenfeld N, Mewes AUJ, Goldberg-Zimring D, Zou KH, Westin C-F, Wells III WM, et al. Capturing Intraoperative Deformations: Research Experience at Brigham and Women's Hospital. Med Image Anal. 2005;9 (2) :145-62.Abstract

During neurosurgical procedures the objective of the neurosurgeon is to achieve the resection of as much diseased tissue as possible while achieving the preservation of healthy brain tissue. The restricted capacity of the conventional operating room to enable the surgeon to visualize critical healthy brain structures and tumor margin has lead, over the past decade, to the development of sophisticated intraoperative imaging techniques to enhance visualization. However, both rigid motion due to patient placement and nonrigid deformations occurring as a consequence of the surgical intervention disrupt the correspondence between preoperative data used to plan surgery and the intraoperative configuration of the patient's brain. Similar challenges are faced in other interventional therapies, such as in cryoablation of the liver, or biopsy of the prostate. We have developed algorithms to model the motion of key anatomical structures and system implementations that enable us to estimate the deformation of the critical anatomy from sequences of volumetric images and to prepare updated fused visualizations of preoperative and intraoperative images at a rate compatible with surgical decision making. This paper reviews the experience at Brigham and Women's Hospital through the process of developing and applying novel algorithms for capturing intraoperative deformations in support of image guided therapy.

Golland P, Grimson EWL, Shenton ME, Kikinis R. Detection and analysis of statistical differences in anatomical shape. Med Image Anal. 2005;9 (1) :69-86.Abstract
We present a computational framework for image-based analysis and interpretation of statistical differences in anatomical shape between populations. Applications of such analysis include understanding developmental and anatomical aspects of disorders when comparing patients versus normal controls, studying morphological changes caused by aging, or even differences in normal anatomy, for example, differences between genders. Once a quantitative description of organ shape is extracted from input images, the problem of identifying differences between the two groups can be reduced to one of the classical questions in machine learning of constructing a classifier function for assigning new examples to one of the two groups while making as few misclassifications as possible. The resulting classifier must be interpreted in terms of shape differences between the two groups back in the image domain. We demonstrate a novel approach to such interpretation that allows us to argue about the identified shape differences in anatomically meaningful terms of organ deformation. Given a classifier function in the feature space, we derive a deformation that corresponds to the differences between the two classes while ignoring shape variability within each class. Based on this approach, we present a system for statistical shape analysis using distance transforms for shape representation and the support vector machines learning algorithm for the optimal classifier estimation and demonstrate it on artificially generated data sets, as well as real medical studies.
Wiegand LC, Warfield SK, Levitt JJ, Hirayasu Y, Salisbury DF, Heckers S, Bouix S, Schwartz D, Spencer M, Dickey CC, et al. An in vivo MRI study of prefrontal cortical complexity in first-episode psychosis. Am J Psychiatry. 2005;162 (1) :65-70.Abstract
OBJECTIVE: The purpose of this study was to investigate abnormalities in the surface complexity of the prefrontal cortex and in the hemispheric asymmetry of cortical complexity in first-episode patients with schizophrenia. METHOD: An estimate of the surface complexity of the prefrontal cortex was derived from the number of voxels along the boundary between gray matter and CSF. Magnetic resonance imaging scans were acquired from patients with a first episode of schizophrenia (N=17), patients with a first episode of affective psychosis (N=17), and normal comparison subjects (N=17), age-matched within a narrow age range (18-29 years). This study group was the focus of a previous study that showed lower prefrontal cortical volume in patients with schizophrenia. RESULTS: Prefrontal cortical complexity was not significantly different among the groups. However, the schizophrenia patients differed significantly from the normal comparison subjects in asymmetry, with the schizophrenia patients showing less left-greater-than-right asymmetry in cortical complexity than the comparison subjects. CONCLUSIONS: An abnormal pattern of asymmetry in the prefrontal cortex of first-episode patients with schizophrenia provides evidence for a neurodevelopmental mechanism in the etiology of schizophrenia.
Limperopoulos C, Soul JS, Gauvreau K, Huppi PS, Warfield SK, Bassan H, Robertson RL, Volpe JJ, du Plessis AJ. Late gestation cerebellar growth is rapid and impeded by premature birth. Pediatrics. 2005;115 (3) :688-95.Abstract
OBJECTIVE: Cognitive impairments and academic failure are commonly reported in survivors of preterm birth. Recent studies suggest an important role for the cerebellum in the development of cognitive and social functions. The objective of this study was to examine the impact of prematurity itself, as well as prematurity-related brain injuries, on early postnatal cerebellar growth with quantitative MRI. METHODS: Advanced 3-dimensional volumetric MRI was performed and cerebellar volumes were obtained by manual outlining in preterm (<37 weeks) and healthy term-born infants. Intracranial and total brain volumes were also calculated. RESULTS: A total of 169 preterm and 20 healthy full-term infants were studied; 145 had preterm MRI (pMRI), 75 had term MRI (tMRI), and 51 underwent both pMRI and tMRI. From 28 weeks' postconceptional age to term, mean cerebellar volume (177%) in preterm infants increased at a much faster rate than did mean intracranial (110%) or mean brain (107%) volumes. Smaller cerebellar volume was significantly related to lower gestational age at birth and to intracranial and total brain volumes. Mean cerebellar volume of preterm infants at tMRI was significantly smaller than the volumes of term-born infants. Cerebellar growth impairment was correlated strongly with associated brain injuries, even in the absence of direct cerebellar injury. CONCLUSIONS: Our data suggest that the growth of the immature cerebellum is particularly rapid during late gestation. However, this accelerated growth seems to be impeded by premature birth and associated brain injury. The long-term neurodevelopmental disabilities seen in survivors of premature birth may be attributable in part to impaired cerebellar development.
Brehmer A, Lindig TM, Schrödl F, Neuhuber W, Ditterich D, Rexer M, Rupprecht H. Morphology of enkephalin-immunoreactive myenteric neurons in the human gut. Histochem Cell Biol. 2005;123 (2) :131-8.Abstract
The aim of this study was the morphological and further chemical characterisation of neurons immunoreactive for leu-enkephalin (leuENK). Ten wholemounts of small and large intestinal segments from nine patients were immunohistochemically triple-stained for leuENK/neurofilament 200 (NF)/substance P (SP). Based on their simultaneous NF-reactivity and 3D reconstruction of single NF-reactive cells, 97.5% of leuENK-positive neurons displayed the appearance of stubby neurons: small somata; short, stubby dendrites and one axon. Of these leuENK-reactive stubby neurons, 91.3% did not display co-reactivity for SP whereas 8.7% were SP-co-reactive. As to their axonal projection pattern, 50.4% of the recorded leuENK stubby neurons had axons running orally whereas in 29.4% they ran anally; the directions of the remaining 20.2% could not be determined. No axons were seen to enter into secondary strands of the myenteric plexus. Somal area measurements revealed clearly smaller somata of leuENK-reactive stubby neurons (between 259+/-47 microm(2) and 487+/-113 microm(2)) than those of putative sensory type II neurons (between 700+/-217 microm(2) and 1,164+/-396 microm(2)). The ratio dendritic field area per somal area of leuENK-reactive stubby neurons was between 2.0 and 2.8 reflecting their short dendrites. Additionally, we estimated the proportion of leuENK-positive neurons in comparison to the putative whole myenteric neuron population in four leuENK/anti-Hu doublestained wholemounts. This proportion ranged between 5.9% and 8.3%. We suggest leuENK-reactive stubby neurons to be muscle motor neurons and/or ascending interneurons. Furthermore, we explain why we do not use the term "Dogiel type I neurons" for this population.
Wolfson L, Wei X, Hall CB, Panzer V, Wakefield D, Benson RR, Schmidt JA, Warfield SK, Guttmann CRG. Accrual of MRI white matter abnormalities in elderly with normal and impaired mobility. J Neurol Sci. 2005;232 (1-2) :23-7.Abstract
White matter signal abnormality (WMSA) is often present in the MRIs of older persons with mobility impairment. We examined the relationship between impaired mobility and the progressive accrual of WMSA. Mobility was assessed with the Short Physical Performance Battery (SPPB) and quantitative measures of gait and balance. Fourteen subjects had baseline and follow-up MRI scans performed 20 months apart. WMSA was detected and quantified using automated computer algorithms. In the control subjects, WMSA volume increased by 0.02+/-0.05% ICCV (percent intracranial cavity volume)/year while the WMSA of mobility impaired subjects increased five-times faster (0.10+/-0.10 ICCV/year, p=0.03). WMSA volume was related to some of the mobility measures and was sensitive to change which was not true of the other MRI variables. The study demonstrates the sensitivity of longitudinal automated volumetric analysis of WMSA to differentiate differences in the accrual rate of WMSA in groups selected on the basis of mobility. Based on these results, we propose that a subset of subjects with mobility impairment have accelerated, disease related WMSA accrual, thus explaining the rapid progression of mobility impairment in some older persons without apparent cause. This study demonstrates that quantitative MRI and performance measures can provide valuable insight into the rate of progression and pathophysiologic abnormalities underlying mobility impairment.
Kubicki M, Park H, Westin CF, Nestor PG, Mulkern RV, Maier SE, Niznikiewicz M, Connor E, Levitt JJ, Frumin M, et al. DTI and MTR Abnormalities in Schizophrenia: Analysis of White Matter Integrity. Neuroimage. 2005;26 (4) :1109-18.Abstract

Diffusion tensor imaging (DTI) studies in schizophrenia demonstrate lower anisotropic diffusion within white matter due either to loss of coherence of white matter fiber tracts, to changes in the number and/or density of interconnecting fiber tracts, or to changes in myelination, although methodology as well as localization of such changes differ between studies. The aim of this study is to localize and to specify further DTI abnormalities in schizophrenia by combining DTI with magnetization transfer imaging (MTI), a technique sensitive to myelin and axonal alterations in order to increase specificity of DTI findings. 21 chronic schizophrenics and 26 controls were scanned using Line-Scan-Diffusion-Imaging and T1-weighted techniques with and without a saturation pulse (MT). Diffusion information was used to normalize co-registered maps of fractional anisotropy (FA) and magnetization transfer ratio (MTR) to a study-specific template, using the multi-channel daemon algorithm, designed specifically to deal with multidirectional tensor information. Diffusion anisotropy was decreased in schizophrenia in the following brain regions: the fornix, the corpus callosum, bilaterally in the cingulum bundle, bilaterally in the superior occipito-frontal fasciculus, bilaterally in the internal capsule, in the right inferior occipito-frontal fasciculus and the left arcuate fasciculus. MTR maps demonstrated changes in the corpus callosum, fornix, right internal capsule, and the superior occipito-frontal fasciculus bilaterally; however, no changes were noted in the anterior cingulum bundle, the left internal capsule, the arcuate fasciculus, or inferior occipito-frontal fasciculus. In addition, the right posterior cingulum bundle showed MTR but not FA changes in schizophrenia. These findings suggest that, while some of the diffusion abnormalities in schizophrenia are likely due to abnormal coherence, or organization of the fiber tracts, some of these abnormalities may, in fact, be attributed to or coincide with myelin/axonal disruption.

du Bois d'Aische A, Craene MD, Geets X, Gregoire V, Macq B, Warfield SK. Efficient multi-modal dense field non-rigid registration: alignment of histological and section images. Med Image Anal. 2005;9 (6) :538-46.Abstract
We describe a new algorithm for non-rigid registration capable of estimating a constrained dense displacement field from multi-modal image data. We applied this algorithm to capture non-rigid deformation between digital images of histological slides and digital flat-bed scanned images of cryotomed sections of the larynx, and carried out validation experiments to measure the effectiveness of the algorithm. The implementation was carried out by extending the open-source Insight ToolKit software. In diagnostic imaging of cancer of the larynx, imaging modalities sensitive to both anatomy (such as MRI and CT) and function (PET) are valuable. However, these modalities differ in their capability to discriminate the margins of tumor. Gold standard tumor margins can be obtained from histological images from cryotomed sections of the larynx. Unfortunately, the process of freezing, fixation, cryotoming and staining the tissue to create histological images introduces non-rigid deformations and significant contrast changes. We demonstrate that the non-rigid registration algorithm we present is able to capture these deformations and the algorithm allows us to align histological images with scanned images of the larynx. Our non-rigid registration algorithm constructs a deformation field to warp one image onto another. The algorithm measures image similarity using a mutual information similarity criterion, and avoids spurious deformations due to noise by constraining the estimated deformation field with a linear elastic regularization term. The finite element method is used to represent the deformation field, and our implementation enables us to assign inhomogeneous material characteristics so that hard regions resist internal deformation whereas soft regions are more pliant. A gradient descent optimization strategy is used and this has enabled rapid and accurate convergence to the desired estimate of the deformation field. A further acceleration in speed without cost of accuracy is achieved by using an adaptive mesh refinement strategy.
Tsai A, Wells III WM, Warfield SK, Willsky AS. An EM Algorithm for Shape Classification Based on Level Sets. Med Image Anal. 2005;9 (5) :491-502.Abstract

In this paper, we propose an expectation-maximization (EM) approach to separate a shape database into different shape classes, while simultaneously estimating the shape contours that best exemplify each of the different shape classes. We begin our formulation by employing the level set function as the shape descriptor. Next, for each shape class we assume that there exists an unknown underlying level set function whose zero level set describes the contour that best represents the shapes within that shape class. The level set function for each example shape in the database is modeled as a noisy measurement of the appropriate shape class's unknown underlying level set function. Based on this measurement model and the judicious introduction of the class labels as the hidden data, our EM formulation calculates the labels for shape classification and estimates the shape contours that best typify the different shape classes. This resulting iterative algorithm is computationally efficient, simple, and accurate. We demonstrate the utility and performance of this algorithm by applying it to two medical applications.

Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin C-F, Kikinis R, et al. Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study. Biol Psychiatry. 2005;58 (6) :468-78.Abstract
BACKGROUND: Using diffusion tensor imaging (DTI), we previously reported abnormalities in two critical white matter tracts in schizophrenia, the uncinate fasciculus (UF) and the cingulum bundle (CB), both related to fronto-temporal connectivity. Here, we investigate these two bundles in unmedicated subjects with schizotypal personality disorder (SPD). METHODS: Fifteen male SPD subjects and 15 male control subjects were scanned with line-scan DTI. Fractional anisotropy (FA) and mean diffusivity (D(m)) were used to quantify water diffusion, and cross-sectional area was defined with a directional threshold method. Exploratory correlation analyses were evaluated with Spearman's rho, followed by post hoc hierarchical regression analyses. RESULTS: We found bilaterally reduced FA in the UF of SPD subjects. For CB, there was no significant group difference for FA or D(m) measures. Additionally, in SPD, reduced FA in the right UF was correlated with clinical symptoms, including ideas of reference, suspiciousness, restricted affect, and social anxiety. In contrast, left UF area was correlated with measures of cognitive function, including general intelligence, verbal and visual memory, and executive performance. CONCLUSIONS: These findings in SPD suggest altered fronto-temporal connectivity through the UF, similar to findings in schizophrenia, and intact neocortical-limbic connectivity through the CB, in marked contrast with what has been reported in schizophrenia.
Limperopoulos C, Soul JS, Haidar H, Huppi PS, Bassan H, Warfield SK, Robertson RL, Moore M, Akins P, Volpe JJ, et al. Impaired trophic interactions between the cerebellum and the cerebrum among preterm infants. Pediatrics. 2005;116 (4) :844-50.Abstract
BACKGROUND: Advanced neuroimaging techniques have brought increasing recognition of cerebellar injury among premature infants. The developmental relationship between early brain injury and effects on the cerebrum and cerebellum remains unclear. OBJECTIVES: To examine whether cerebral parenchymal brain lesions among preterm infants are associated with subsequent decreases in cerebellar volume and, conversely, whether primary cerebellar injury is associated with decreased cerebral brain volumes, with advanced, 3-dimensional, volumetric MRI at term gestational age equivalent. METHODS: Total cerebellar volumes and cerebellar gray and myelinated white matter volumes were determined through manual outlining for 74 preterm infants with unilateral periventricular hemorrhagic infarction (14 infants), bilateral diffuse periventricular leukomalacia (20 infants), cerebellar hemorrhage (10 infants), or normal term gestational age equivalent MRI findings (30 infants). Total brain and right/left cerebral and cerebellar hemispheric volumes were calculated. RESULTS: Unilateral cerebral brain injury was associated with significantly decreased volume of the contralateral cerebellar hemisphere. Conversely, unilateral primary cerebellar injury was associated with a contralateral decrease in supratentorial brain volume. Cerebellar gray matter and myelinated white matter volumes were reduced significantly not only among preterm infants with primary cerebellar hemorrhage but also among infants with cerebral parenchymal brain injury. CONCLUSIONS: These data suggest strongly that both reduction in contralateral cerebellar volume with unilateral cerebral parenchymal injury and reduction in total cerebellar volume with bilateral cerebral lesions are related to trophic transsynaptic effects. Early-life cerebellar injury may contribute importantly to the high rates of cognitive, behavioral, and motor deficits reported for premature infants.
Verhey JF, Wisser J, Warfield SK, Rexilius J, Kikinis R. Non-rigid registration of a 3D ultrasound and a MR image data set of the female pelvic floor using a biomechanical model. Biomed Eng Online. 2005;4 :19.Abstract
BACKGROUND: The visual combination of different modalities is essential for many medical imaging applications in the field of Computer-Assisted medical Diagnosis (CAD) to enhance the clinical information content. Clinically, incontinence is a diagnosis with high clinical prevalence and morbidity rate. The search for a method to identify risk patients and to control the success of operations is still a challenging task. The conjunction of magnetic resonance (MR) and 3D ultrasound (US) image data sets could lead to a new clinical visual representation of the morphology as we show with corresponding data sets of the female anal canal with this paper. METHODS: We present a feasibility study for a non-rigid registration technique based on a biomechanical model for MR and US image data sets of the female anal canal as a base for a new innovative clinical visual representation. RESULTS: It is shown in this case study that the internal and external sphincter region could be registered elastically and the registration partially corrects the compression induced by the ultrasound transducer, so the MR data set showing the native anatomy is used as a frame for the US data set showing the same region with higher resolution but distorted by the transducer CONCLUSION: The morphology is of special interest in the assessment of anal incontinence and the non-rigid registration of normal clinical MR and US image data sets is a new field of the adaptation of this method incorporating the advantages of both technologies.
Friman O, Westin C-F. Resampling fMRI time series. Neuroimage. 2005;25 (3) :859-67.Abstract
The problem of selecting a threshold for the statistical parameter maps in functional MRI (fMRI) is a delicate issue. The use of advanced test statistics and/or the complex dependence structure of fMRI noise may preclude parametric statistical methods for finding appropriate thresholds. Non-parametric statistical methodology has been presented as a feasible alternative. In this paper, we discuss resampling methods for finding thresholds in single subject fMRI analysis. It is shown that the presence of a BOLD response in the time series biases the estimation of the temporal autocorrelation, which in turn leads to biased thresholds. Therefore, proposed resampling methods based on Fourier and wavelet transforms, which employ implicit and weak models of the temporal noise characteristic, may produce erroneous thresholds. In contrast, resampling based on a pre-whitening transform, which is driven by an explicit noise model, is robust to the presence of a BOLD response. The size of the bias is, however, largely dependent on the complexity of the experimental design. While blocked designs can induce large biases, event-related designs generate significantly smaller biases. Results supporting these claims are provided.
Zou KH, Tuncali K, Warfield SK, Zentai CP, Worku D, Morrison PR, Silverman SG. Three-dimensional assessment of MR imaging-guided percutaneous cryotherapy using multi-performer repeated segmentations: the value of supervised learning. Acad Radiol. 2005;12 (4) :444-50.Abstract
RATIONALE AND OBJECTIVES: Accurate and reproducible segmentations of two-dimensional images are an important prerequisite for assessing tumor ablations three dimensionally (3D). We evaluated whether supervised learning methods would improve multiperformer repeated segmentations of magnetic resonance images (MRI) obtained before and after MRI-guided cryotherapy of renal cell carcinoma. MATERIALS AND METHODS: Three medical students independently performed five manual segmentations of a biopsy-proven renal cell carcinoma that was treated with percutaneous MRI-guided cryotherapy. Using pretreatment (T2-weighted fast recovery fast spin echo [FRFSE]) and posttreatment (T1-weighted, fat-suppressed, dynamically enhanced) MRIs, regions of tumor cryonecrosis were segmented. The same tasks were repeated after an experienced abdominal radiologist provided supervised learning. Segmentation sensitivity was compared with an estimated 3D-ground truth via voxel counts for regions of tumor, both before and after treatment, and for the regions of cryonecrosis. The sensitivity of each repeated segmentation was compared against the estimated ground truth using sensitivity, overlap index, and volume (mL). RESULTS: Supervised learning significantly improved posttreatment segmentation sensitivity (P = .03). With supervised learning, the ranges of the performance metrics over the segmentation performers were: pretreated tumor, sensitivity 0.902-0.999, overlap index 0.935-0.961, and volume 19.15-23.71 mL; posttreated tumor, sensitivity 0.923-0.991, overlap index 0.952-0.981, and volume 20.67-22.70 mL; in the ablation zone, sensitivity 0.938-0.969, overlap index 0.940-0.962, and volume 31.79-32.36 mL. CONCLUSIONS: Supervised learning improved multiperformer repeated segmentations of MRIs obtained before and after MRI-guided percutaneous cryotherapy of renal cell carcinoma. These methods may prove useful in aiding the 3D assessment of percutaneous tumor ablations.
Goldberg-Zimring D, Mewes AUJ, Maddah M, Warfield SK. Diffusion tensor magnetic resonance imaging in multiple sclerosis. J Neuroimaging. 2005;15 (4 Suppl) :68S-81S.Abstract
Multiple sclerosis (MS), a demyelinating disease, occurs principally in the white matter (WM) of the central nervous system. Conventional magnetic resonance imaging (MRI) is sensitive to some, but not all, brain changes associated with MS. Diffusion-weighted imaging (DWI) provides information about water diffusion in tissue and diffusion tensor MRI (DT-MRI) about fiber direction, allowing for the identification of WM abnormalities that are not apparent on conventional MRI images. These techniques can quantitatively characterize the local microstructure of tissues. MS-associated disease processes lead to regions characterized by an increased amount of water diffusion and a decrease in the anisotropy of diffusion direction. These changes have been found to produce different patterns in MS patients presenting different courses of the disease. Changes in water diffusion may allow examination of the type, appearance, enhancement, and location of lesions not readily visible by other means. Ongoing studies of MS are integrating conventional MRI and DT-MRI measures with connectivity-based regional assessment, aiming to provide a better understanding of the nature and the location of WM lesions. This integration and the development of novel image-processing and visualization techniques may improve the understanding of WM architecture and its disruption in MS. This article presents a brief history of DWI, its basic principles and applications in the study of MS, a review of the properties and applications of DT-MRI, and their use in the study of MS. In addition, this article illustrates the methodology for the analysis of DT-MRI in ongoing studies of MS.
Niethammer M, Vela PA, Tannenbaum A. On the Evolution of Vector Distance Functions of Closed Curves. Int J Comput Vis. 2005;65 (1-2) :5-27.Abstract
Inspired by the work by Gomes et al., we describe and analyze a vector distance function approach for the implicit evolution of closed curves of codimension larger than one. The approach is set up in complete generality, and then applied to the evolution of dynamic geometric active contours in [Formula: see text] (codimension three case). In order to carry this out one needs an explicit expression for the zero level set for which we propose a discrete connectivity method. This leads us to make connections with the new theory of cubical homology. We provide some explicit simulation results in order to illustrate the methodology.
Simmross-Wattenberg F, Carranza-Herrezuelo N, Palacios-Camarero C, Casaseca-de-la-Higuera P, Martín-Fernández MA, Aja-Fernández S, Ruiz-Alzola J, Westin C-F, Alberola-López C. Group-Slicer: a collaborative extension of 3D-Slicer. J Biomed Inform. 2005;38 (6) :431-42.Abstract
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.
Liu L, Meier D, Polgar-Turcsanyi M, Karkocha P, Bakshi R, Guttmann CRG. Multiple sclerosis medical image analysis and information management. J Neuroimaging. 2005;15 (4 Suppl) :103S-117S.Abstract
Magnetic resonance imaging (MRI) has become a central tool for patient management, as well as research, in multiple sclerosis (MS). Measurements of disease burden and activity derived from MRI through quantitative image analysis techniques are increasingly being used. There are many complexities and challenges in building computerized processing pipelines to ensure efficiency, reproducibility, and quality control for MRI scans from MS patients. Such paradigms require advanced image processing and analysis technologies, as well as integrated database management systems to ensure the most utility for clinical and research purposes. This article reviews pipelines available for quantitative clinical MRI research in MS, including image segmentation, registration, time-series analysis, performance validation, visualization techniques, and advanced medical imaging software packages. To address the complex demands of the sequential processes, the authors developed a workflow management system that uses a centralized database and distributed computing system for image processing and analysis. The implementation of their system includes a web-form-based Oracle database application for information management and event dispatching, and multiple modules for image processing and analysis. The seamless integration of processing pipelines with the database makes it more efficient for users to navigate complex, multistep analysis protocols, reduces the user's learning curve, reduces the time needed for combining and activating different computing modules, and allows for close monitoring for quality-control purposes. The authors' system can be extended to general applications in clinical trials and to routine processing for image-based clinical research.
Clatz O, Sermesant M, Bondiau P-Y, Delingette H, Warfield SK, Malandain G, Ayache N. Realistic simulation of the 3-D growth of brain tumors in MR images coupling diffusion with biomechanical deformation. IEEE Trans Med Imaging. 2005;24 (10) :1334-46.Abstract
We propose a new model to simulate the three-dimensional (3-D) growth of glioblastomas multiforma (GBMs), the most aggressive glial tumors. The GBM speed of growth depends on the invaded tissue: faster in white than in gray matter, it is stopped by the dura or the ventricles. These different structures are introduced into the model using an atlas matching technique. The atlas includes both the segmentations of anatomical structures and diffusion information in white matter fibers. We use the finite element method (FEM) to simulate the invasion of the GBM in the brain parenchyma and its mechanical interaction with the invaded structures (mass effect). Depending on the considered tissue, the former effect is modeled with a reaction-diffusion or a Gompertz equation, while the latter is based on a linear elastic brain constitutive equation. In addition, we propose a new coupling equation taking into account the mechanical influence of the tumor cells on the invaded tissues. The tumor growth simulation is assessed by comparing the in-silico GBM growth with the real growth observed on two magnetic resonance images (MRIs) of a patient acquired with 6 mo difference. Results show the feasibility of this new conceptual approach and justifies its further evaluation.