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Biomedical subjects

Ron Kikinis

Publications and source records attributed to Ron Kikinis.

At least 37 records · Page 2Linked to original sources
PubMed2005

Hybrid formulation of the model-based non-rigid registration problem to improve accuracy and robustness.

We present a new algorithm to register 3D pre-operative Magnetic Resonance (MR) images with intra-operative MR images of the brain. This algorithm relies on a robust estimation of the deformation from a sparse set of measured displacements. We propose a new framework to compute iteratively the displacement field starting from an approximation formulation (minimizing the sum of a regularization term and a data error term) and converging toward an interpolation formulation (least square minimization of the data error term). The robustness of the algorithm is achieved through the introduction of an outliers rejection step in this gradual registration process. We ensure the validity of the deformation by the use of a biomechanical model of the brain specific to the patient, discretized with the finite element method. The algorithm has been tested on six cases of brain tumor resection, presenting a brain shift up to 13 mm.

Algorithms↗
PubMed2005

Brain shift computation using a fully nonlinear biomechanical model.

In the present study, fully nonlinear (i.e. accounting for both geometric and material nonlinearities) patient specific finite element brain model was applied to predict deformation field within the brain during the craniotomy-induced brain shift. Deformation of brain surface was used as displacement boundary conditions. Application of the computed deformation field to align (i.e. register) the preoperative images with the intraoperative ones indicated that the model very accurately predicts the displacements of gravity centers of the lateral ventricles and tumor even for very limited information about the brain surface deformation. These results are sufficient to suggest that nonlinear biomechanical models can be regarded as one possible way of complementing medical image processing techniques when conducting nonrigid registration. Important advantage of such models over the linear ones is that they do not require unrealistic assumptions that brain deformations are infinitesimally small and brain tissue stress-strain relationship is linear.

Biomechanical Phenomena↗
PubMed2005

Rigid overlay of volume sonography and MR image data of the female pelvic floor using a fiducial based alignment--feasibility due to a case series.

The visual combination of different medical image acquisition techniques (modalities) can lead to new modalities with enhanced informative content. In this paper, we present an overlay technique of magnetic resonance (MR) and 3D US image data sets of the female anal canal (internal and external sphincter) as a base for a new diagnostic modality. It is a new field of the application of the overlay technique. Three corresponding MR and US volume data sets from the female pelvic floor region were filtered using adaptive filtering techniques and overlayed (=registered rigidly) with a landmark based alignment method.

Feasibility Studies↗
PubMed2005

Analysis of skeletal movements in mandibular distraction osteogenesis.

PURPOSE: The purpose of this study was to use geometric parameters of movement, calculated from 3-dimensional computed tomography (CT) data, to determine the curvilinear distractor dimensions required to correct mandibular deformities in a series of patients. MATERIALS AND METHODS: Preoperative CT scans from 15 patients with symmetric (n = 5) and asymmetric (n = 10) deformities were imported into a CT-based software program (Osteoplan; an open-source visualization application developed by Gering et al at the Surgical Planning Laboratory [SPL, Brigham and Womens Hospital, Boston, MA]). The software was used to reconstruct virtual 3-dimensional models from these scans. Two experienced surgeons, working with a computer scientist, then used Osteoplan to create an ideal treatment plan for each patient. In each case, the 3-dimensional curvilinear movement was quantified using 4 "parameters of movement" (POMs). These parameters were then used to prescribe a distraction device capable of executing the planned skeletal correction. Curvilinear distractor dimensions calculated by Osteoplan included the radius of curvature of the prescribed device, and the distractor elongation, pitch, and handedness. RESULTS: Treatment plans including POMs were developed for each patient. The radii of curvature for the prescribed distractors ranged from 2.3 to 14.1 cm, the distractor elongation dimensions ranged from 0.7 to 3.2 cm, and the pitch (horizontal plane) dimensions ranged from 0.005 to 0.8 cm. Handedness was either a left (n = 12) or right (n = 8) turning helix. CONCLUSION: The results of this study indicate that, using geometric parameters of movement calculated from 3-dimensional CT scans, curvilinear devices could be prescribed for correction of the range of skeletal deformities in this group of patients.

Computer Simulation↗
PubMed2005

Detection and analysis of statistical differences in anatomical shape.

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.

Algorithms↗
PubMed2005

Robust nonrigid registration to capture brain shift from intraoperative MRI.

We present a new algorithm to register 3-D preoperative magnetic resonance (MR) images to intraoperative MR images of the brain which have undergone brain shift. This algorithm relies on a robust estimation of the deformation from a sparse noisy set of measured displacements. We propose a new framework to compute the displacement field in an iterative process, allowing the solution to gradually move from an approximation formulation (minimizing the sum of a regularization term and a data error term) to an interpolation formulation (least square minimization of the data error term). An outlier rejection step is introduced in this gradual registration process using a weighted least trimmed squares approach, aiming at improving the robustness of the algorithm. We use a patient-specific model discretized with the finite element method in order to ensure a realistic mechanical behavior of the brain tissue. To meet the clinical time constraint, we parallelized the slowest step of the algorithm so that we can perform a full 3-D image registration in 35 s (including the image update time) on a heterogeneous cluster of 15 personal computers. The algorithm has been tested on six cases of brain tumor resection, presenting a brain shift of up to 14 mm. The results show a good ability to recover large displacements, and a limited decrease of accuracy near the tumor resection cavity.

Algorithms↗
PubMed2005

Reproducibility of functional MR imaging: preliminary results of prospective multi-institutional study performed by Biomedical Informatics Research Network.

PURPOSE: To prospectively investigate the factors--including subject, brain hemisphere, study site, field strength, imaging unit vendor, imaging run, and examination visit--affecting the reproducibility of functional magnetic resonance (MR) imaging activations based on a repeated sensory-motor (SM) task. MATERIALS AND METHODS: The institutional review boards of all participating sites approved this HIPAA-compliant study. All subjects gave informed consent. Functional MR imaging data were repeatedly acquired from five healthy men aged 20-29 years who performed the same SM task at 10 sites. Five 1.5-T MR imaging units, four 3.0-T units, and one 4.0-T unit were used. The subjects performed bilateral finger tapping on button boxes with a 3-Hz audio cue and a reversing checkerboard. In a block design, 15-second epochs of alternating baseline and tasks yielded 85 acquisitions per run. Functional MR images were acquired with block-design echo-planar or spiral gradient-echo sequences. Brain activation maps standardized in a unit-sphere for the left and right hemispheres of each subject were constructed. Areas under the receiver operating characteristic curve, intraclass correlation coefficients, multiple regression analysis, and paired Student t tests were used for statistical analyses. RESULTS: Significant factors were subject (P < .005), k-space (P < .005), and field strength (P = .02) for sensitivity and subject (P = .03) and k-space (P = .05) for specificity. At 1.5-T MR imaging, mean sensitivities ranged from 7% to 32% and mean specificities were higher than 99%. At 3.0 T, mean sensitivities and specificities ranged from 42% to 85% and from 96% to 99%, respectively. At 4.0 T, mean sensitivities and specificities ranged from 41% to 73% and from 95% to 99%, respectively. Mean areas under the receiver operating characteristic curve (+/- their standard errors) were 0.77 +/- 0.05 at 1.5 T, 0.90 +/- 0.09 at 3.0 T, and 0.95 +/- 0.02 at 4.0 T, with significant differences between the 1.5- and 3.0-T examinations and between the 1.5- and 4.0-T examinations (P < .01 for both comparisons). Intraclass correlation coefficients ranged from 0.49 to 0.71. CONCLUSION: MR imaging at 3.0- and 4.0-T yielded higher reproducibility across sites and significantly better results than 1.5-T imaging. The effects of subject, k-space, and field strength on examination reproducibility were significant.

Adult↗
PubMed2005

An in vivo MRI study of prefrontal cortical complexity in first-episode psychosis.

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.

Adolescent↗
PubMed2004

Capturing intraoperative deformations: research experience at Brigham and Women's Hospital.

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.

Algorithms↗
PubMed2004

Cavum septi pellucidi in first-episode schizophrenia and first-episode affective psychosis: an MRI study.

A high prevalence of abnormal cavum septi pellucidi (CSP) in schizophrenia may reflect neurodevelopmental abnormalities in midline structures of the brain. The relationship, however, between abnormal CSP and clinical symptoms, and with abnormalities in other limbic structures remains unclear, as does the question of whether a similar abnormality is present in affective psychosis. Seventy-four patients at their first hospitalization, 33 with schizophrenia and 41 with affective (mainly manic) psychosis, and 56 healthy control subjects underwent high-spatial-resolution magnetic resonance imaging (MRI). CSP on six slices or more on 0.9375-mm resampled coronal images was categorized as abnormal. The prevalence of abnormal CSP in both schizophrenic patients (26.1%) and affective psychosis patients (18.2%) was significantly higher than was observed in control subjects (8.2%). In schizophrenic patients only, larger CSP was significantly associated with more severe thinking disturbance and smaller left parahippocampal gyrus gray matter volumes. While the relationships between CSP ratings and clinical symptoms did not significantly differ between the two psychosis groups as assessed by the comparison of regression slopes, the association with limbic volumes appeared to be specific to schizophrenic patients. These results suggest that psychosis associated with schizophrenia and affective disorder share, at least to some extent, neurodevelopmental abnormalities involving midline structures and associated psychopathological consequences. However, the association between abnormal CSP and limbic systems may be more specific to schizophrenia.

Adolescent↗
PubMed2004

Three validation metrics for automated probabilistic image segmentation of brain tumours.

The validity of brain tumour segmentation is an important issue in image processing because it has a direct impact on surgical planning. We examined the segmentation accuracy based on three two-sample validation metrics against the estimated composite latent gold standard, which was derived from several experts' manual segmentations by an EM algorithm. The distribution functions of the tumour and control pixel data were parametrically assumed to be a mixture of two beta distributions with different shape parameters. We estimated the corresponding receiver operating characteristic curve, Dice similarity coefficient, and mutual information, over all possible decision thresholds. Based on each validation metric, an optimal threshold was then computed via maximization. We illustrated these methods on MR imaging data from nine brain tumour cases of three different tumour types, each consisting of a large number of pixels. The automated segmentation yielded satisfactory accuracy with varied optimal thresholds. The performances of these validation metrics were also investigated via Monte Carlo simulation. Extensions of incorporating spatial correlation structures using a Markov random field model were considered.

Algorithms↗
PubMed2004

Magnetic resonance imaging based colonography for diagnosis and assessment of diverticulosis and diverticulitis.

BACKGROUND AND AIMS: MRI-based colonography is a new minimally invasive imaging modality to assess the colon and abdomen. This new method which is applied mainly for polyp screening could be an integrative approach for colonic diverticulitis assessment. This study evaluated the feasibility of MRI-based colonography to assess diverticulosis or diverticulitis. PATIENTS AND METHODS: Fourteen consecutive patients with clinically suspected diverticulitis were examined by MRI colonography on a 1.5-T scanner. All patients underwent abdominal CT as gold standard. N-Butyl-scopalamin was given intravenously to reduce bowel peristalsis. After rectal administration of a T1-positive enema T1- and T2-weighted acquisitions with additional intravenous contrast were obtained. A 3D FLASH sequence was acquired for virtual colonography. The results were compared with CT and biological parameters such as white blood cell count and C-reactive protein. RESULTS: Of 56 bowel segments (sigmoid colon, descending colon, transverse colon, ascending colon) in all 14 patients 54 were assessed to have good to fair image quality. Having CT as standard of reference, all sigmoid diverticula were diagnosed based on MRI. Inflammation as judged by CT was identically assessed on MRI. 3D models of the colon revealed further diverticula in the remaining colon; additionally, the 3D models gave a comprehensive image for surgical planning. CONCLUSION: In our preliminary study MRI colonography revealed the same diagnosis as CT in all patients without ionizing radiation. Additionally, 3D-rendered models and virtual colonoscopy can be performed. This comprehensive 3D models could replace presurgical planning barium enema with concurrent assessment of the residual colon.

Adult↗
PubMed2004

Prefrontal cortical thickness in first-episode psychosis: a magnetic resonance imaging study.

BACKGROUND: Findings from postmortem studies suggest reduced prefrontal cortical thickness in schizophrenia; however, cortical thickness in first-episode schizophrenia has not been evaluated using magnetic resonance imaging (MRI). METHODS: Prefrontal cortical thickness was measured using MRI in first-episode schizophrenia patients (n = 17), first-episode affective psychosis patients (n = 17), and normal control subjects (n = 17); subjects were age-matched within 2 years and within a narrow age range (18-29 years). A previous study using the same subjects reported reduced prefrontal gray matter volume in first-episode schizophrenia. Manual editing was performed on those prefrontal segmentations before cortical thickness was measured. RESULTS: Prefrontal cortical thickness was not significantly different among groups. Prefrontal gray matter volume and thickness were, however, positively correlated in both schizophrenia and control subjects. The product of boundary complexity and thickness, an alternative measure of volume, was positively correlated with volume for all three groups. Finally, age and age at first medication were negatively correlated with prefrontal cortical thickness only in first-episode schizophrenia. CONCLUSIONS: This study demonstrates the potential usefulness of MRI for the study of cortical thickness abnormalities in schizophrenia. Correlations between cortical thickness and age and between cortical thickness and age at first medication suggest that the longer the schizophrenic process has been operative, the thinner the prefrontal cortex, although this needs confirmation in a longitudinal study.

Adolescent↗
PubMed2004

Shape of caudate nucleus and its cognitive correlates in neuroleptic-naive schizotypal personality disorder.

BACKGROUND: We measured the shape of the head of the caudate nucleus with a new approach based on magnetic resonance imaging (MRI) in schizotypal personality disorder (SPD) subjects in whom we previously reported decreased caudate nucleus volume. We believe MRI shape analysis complements traditional MRI volume measurements. METHODS: Magnetic resonance imaging scans were used to measure the shape of the caudate nucleus in 15 right-handed male subjects with SPD, who had no prior neuroleptic exposure, and in 14 matched normal comparison subjects. With MRI processing tools, we measured the head of the caudate nucleus using a shape index, which measured how much a given shape deviates from a sphere. RESULTS: In relation to comparison subjects, neuroleptic never-medicated SPD subjects had significantly higher (more "edgy") head of the caudate shape index scores, lateralized to the right side. Additionally, for SPD subjects, higher right and left head of the caudate SI scores correlated significantly with poorer neuropsychological performance on tasks of visuospatial memory and auditory/verbal working memory, respectively. CONCLUSIONS: These data confirm the value of measuring shape, as well as volume, of brain regions of interest and support the association of intrinsic pathology in the caudate nucleus, unrelated to neuroleptic medication, with cognitive abnormalities in the schizophrenia spectrum.

Adult↗
PubMed2004

A statistically based flow for image segmentation.

In this paper we present a new algorithm for 3D medical image segmentation. The algorithm is versatile, fast, relatively simple to implement, and semi-automatic. It is based on minimizing a global energy defined from a learned non-parametric estimation of the statistics of the region to be segmented. Implementation details are discussed and source code is freely available as part of the 3D Slicer project. In addition, a new unified set of validation metrics is proposed. Results on artificial and real MRI images show that the algorithm performs well on large brain structures both in terms of accuracy and robustness to noise.

Algorithms↗
PubMed2004

An MRI study of spatial probability brain map differences between first-episode schizophrenia and normal controls.

We created a spatial probability atlas of schizophrenia to provide information about the neuroanatomic variability of brain regions of patients with the disorder. Probability maps of 16 regions of interest (ROIs) were constructed by taking manually parcellated ROIs from subjects' magnetic resonance images (MRIs) and linearly transforming them into Talairach space using the Montreal Neurological Institute (MNI) template. ROIs included temporal, parietal, and prefrontal cortex subregions, with a principal focus on temporal lobe structures. Subject Ns ranged from 11 to 28 for the different ROIs. Our global measure of the spatial distribution of the transformed ROI was the sum of voxels with 50% overlap among subjects. The superior temporal gyrus (STG) and fusiform gyrus (FG) had lower values for schizophrenic subjects than for normal controls, suggestive of greater spatial variability for these ROIs in schizophrenic subjects. For the computation of statistical significance of group differences in portions of the ROI, we used voxel-wise comparisons and Fisher's exact test. First-episode schizophrenic patients compared with controls showed lower probability (P < 0.05) at dorso-posterior areas of planum temporale and Heschl's gyrus, lateral and anterior regions in the left hippocampus (HIPP), and dorsolateral regions of fusiform gyrus. Importantly, most ROIs of schizophrenic subjects showed a significantly lower spatial overlap than controls, even after nonlinear spatial normalization, suggesting a greater heterogeneity in the spatial distribution of ROIs. There is consequently a need for caution in neuroimaging studies where data from schizophrenic subjects are normalized to a particular stereotaxic coordinate system based on healthy controls. Apparent group differences in activation may simply reflect a greater heterogeneity of spatial distribution in schizophrenia.

Adult↗
PubMed2004

White matter hemisphere asymmetries in healthy subjects and in schizophrenia: a diffusion tensor MRI study.

Hemisphere asymmetry was explored in normal healthy subjects and in patients with schizophrenia using a novel voxel-based tensor analysis applied to fractional anisotropy (FA) of the diffusion tensor. Our voxel-based approach, which requires precise spatial normalization to remove the misalignment of fiber tracts, includes generating a symmetrical group average template of the diffusion tensor by applying nonlinear elastic warping of the demons algorithm. We then normalized all 32 diffusion tensor MRIs from healthy subjects and 23 from schizophrenic subjects to the symmetrical average template. For each brain, six channels of tensor component images and one T2-weighted image were used for registration to match tensor orientation and shape between images. A statistical evaluation of white matter asymmetry was then conducted on the normalized FA images and their flipped images. In controls, we found left-higher-than-right anisotropic asymmetry in the anterior part of the corpus callosum, cingulum bundle, the optic radiation, and the superior cerebellar peduncle, and right-higher-than-left anisotropic asymmetry in the anterior limb of the internal capsule and the anterior limb's prefrontal regions, in the uncinate fasciculus, and in the superior longitudinal fasciculus. In patients, the asymmetry was lower, although still present, in the cingulum bundle and the anterior corpus callosum, and not found in the anterior limb of the internal capsule, the uncinate fasciculus, and the superior cerebellar peduncle compared to healthy subjects. These findings of anisotropic asymmetry pattern differences between healthy controls and patients with schizophrenia are likely related to neurodevelopmental abnormalities in schizophrenia.

Adult↗