Biomedical subjects

M Sonka

Publications and source records attributed to M Sonka.

At least 19 recordsLinked to original sources

PubMed2001

Highly automated segmentation of arterial and venous trees from three-dimensional magnetic resonance angiography (MRA).

With the development of new magnetic resonance (MR) contrast agents that have longer persistence in the blood, contrast-enhanced magnetic resonance angiography (MRA) facilitates non-invasive imaging of the cardiovascular system at high resolution in large anatomic volumes. These high resolution 'steady state' images have simultaneous enhancement of both the artery and vein blood pools. Consequently, separation of arteries and veins is an emerging challenge in MRA analysis. Because of the complexity of the vascular structure, manual approaches to cardiovascular tree analysis are impractical. A novel, highly-automated low extremity vessel segmentation and display methodology is reported that consists of five main steps: (1) Binary mask generation, (2) tree-structure generation, (3) optimal vessel path calculation, (4) vessel segment labeling, and (5) conflict resolution. The method's performance was tested in computer phantoms and in in vivo data sets. In the computer-generated phantoms, vessel volume errors ranged from 1.0 to 8.8%. In the in vivo data, the labeling errors ranged from 0.1 to 15.5%. The method provided high quality results in individual data sets and demonstrated segmentation robustness.

Abdomen↗

PubMed2001

Multistage hybrid active appearance model matching: segmentation of left and right ventricles in cardiac MR images.

A fully automated approach to segmentation of the left and right cardiac ventricles from magnetic resonance (MR) images is reported. A novel multistage hybrid appearance model methodology is presented in which a hybrid active shape model/active appearance model (AAM) stage helps avoid local minima of the matching function. This yields an overall more favorable matching result. An automated initialization method is introduced making the approach fully automated. Our method was trained in a set of 102 MR images and tested in a separate set of 60 images. In all testing cases, the matching resulted in a visually plausible and accurate mapping of the model to the image data. Average signed border positioning errors did not exceed 0.3 mm in any of the three determined contours-left-ventricular (LV) epicardium, LV and right-ventricular (RV) endocardium. The area measurements derived from the three contours correlated well with the independent standard (r = 0.96, 0.96, 0.90), with slopes and intercepts of the regression lines close to one and zero, respectively. Testing the reproducibility of the method demonstrated an unbiased performance with small range of error as assessed via Bland-Altman statistic. In direct border positioning error comparison, the multistage method significantly outperformed the conventional AAM (p < 0.001). The developed method promises to facilitate fully automated quantitative analysis of LV and RV morphology and function in clinical setting.

Computer Simulation↗

PubMed2000

Object localization and border detection criteria design in edge-based image segmentation: automated learning from examples.

This paper provides methodology for fully automated model-based image segmentation. All information necessary to perform image segmentation is automatically derived from a training set that is presented in a form of segmentation examples. The training set is used to construct two models representing the objects--shape model and border appearance model. A two-step approach to image segmentation is reported. In the first step, an approximate location of the object of interest is determined. In the second step, accurate border segmentation is performed. The shape-variant Hough transform method was developed that provides robust object localization automatically. It finds objects of arbitrary shape, rotation, or scaling and can handle object variability. The border appearance model was developed to automatically design cost functions that can be used in the segmentation criteria of edge-based segmentation methods. Our method was tested in five different segmentation tasks that included 489 objects to be segmented. The final segmentation was compared to manually defined borders with good results [rms errors in pixels: 1.2 (cerebellum), 1.1 (corpus callosum), 1.5 (vertebrae), 1.4 (epicardial), and 1.6 (endocardial) borders]. Two major problems of the state-of-the-art edge-based image segmentation algorithms were addressed: strong dependency on a close-to-target initialization, and necessity for manual redesign of segmentation criteria whenever new segmentation problem is encountered.

Algorithms↗

PubMed1999

Biplane X-ray angiograms, intravascular ultrasound, and 3D visualization of coronary vessels.

The technology for determination of the 3D vascular tree and quantitative characterization of the vessel lumen and vessel wall has become available. With this technology, cardiologists will no longer rely primarily on visual inspection of coronary angiograms but use sophisticated modeling techniques combining images from various modalities for the evaluation of coronary artery disease and the effects of treatment. Techniques have been developed which allow the calculation of the imaging geometry and the 3D position of the vessel centerlines of the vascular tree from biplane views without a calibration object, i.e., from the images themselves, removing the awkwardness of moving the patient to obtain 3D information. With the geometry and positional information, techniques for reconstructing the vessel lumen can now be applied that provide more accurate estimates of the area and shape of the vessel lumen. In conjunction with these developments, techniques have been developed for combining information from intravascular ultrasound images with the information obtained from angiography. The combination of these technologies will yield a more comprehensive characterization and understanding of coronary artery disease and should lead to improved and perhaps less invasive patient care.

Coronary Angiography↗

PubMed1999

Fusion of angiography and intravascular ultrasound in vivo: establishing the absolute 3-D frame orientation.

Data fusion of biplane angiography and intravascular ultrasound (IVUS) facilitates geometrically correct reconstruction of coronary vessels. The locations of IVUS frames along the catheter pullback trajectory can be identified, however the IVUS image orientations remain ambiguous. An automated approach to determination of correct IVUS image orientation in three-dimensional space is reported. Analytical calculation of the catheter twist is followed by statistical optimization determining the absolute IVUS image orientation. The fusion method was applied to data acquired in patients undergoing routine coronary intervention, demonstrating the feasibility and good performance of our approach.

Algorithms↗

PubMed1999

Geometrically correct 3-D reconstruction of intravascular ultrasound images by fusion with biplane angiography--methods and validation.

In the rapidly evolving field of intravascular ultrasound (IVUS), the assessment of vessel morphology still lacks a geometrically correct three-dimensional (3-D) reconstruction. The IVUS frames are usually stacked up to form a straight vessel, neglecting curvature and the axial twisting of the catheter during the pullback. Our method combines the information about vessel cross-sections obtained from IVUS with the information about the vessel geometry derived from biplane angiography. First, the catheter path is reconstructed from its biplane projections, resulting in a spatial model. The locations of the IVUS frames are determined and their orientations relative to each other are calculated using a discrete approximation of the Frenet-Serret formulas known from differential geometry. The absolute orientation of the frame set is established, utilizing the imaging catheter itself as an artificial landmark. The IVUS images are segmented, using our previously developed algorithm. The fusion approach has been extensively validated in computer simulations, phantoms, and cadaveric pig hearts.

Animals↗

PubMed1999

Interstitial lung disease: A quantitative study using the adaptive multiple feature method.

We have previously described an adaptive multiple feature method (AMFM) for the objective assessment of global and regional changes in pulmonary parenchyma to detect emphysema. This computerized method uses a combination of statistical and fractal texture features for characterization of lung tissues based upon high resolution computed tomography (HRCT) scans. This present study was a substantial extension of the AMFM to simultaneously discriminate between multiple pulmonary disease processes. Normal subjects and those with emphysema, idiopathic pulmonary fibrosis (IPF), or sarcoidosis were studied. The AMFM was compared with two currently utilized computer-based methods: mean lung density (MLD) and the histogram analysis (HIST). Globally, when comparing two-subject groups the AMFM overall accuracy was 2 to 18% better than the overall accuracy of MLD and as much as 36% better than the accuracy of the HIST methods. In three-subject group discrimination tasks, the AMFM performed 7 to 27% better than the MLD and 4 to 36% better than the HIST methods. Finally, in discriminating all four subject groups at a time, the AMFM overall accuracy was 81%, which was 21% better than the MLD and 25% better than the HIST method. In most three-subject group comparisons and in the four-subject group comparison, the AMFM was significantly (p < 0.01) better than the MLD and HIST methods. Next, the AMFM was applied to local discrimination between normal and each disease group individually. The normal versus emphysema, normal versus IPF, and normal versus sarcoidosis samples were discriminated with an accuracy of 95, 86, and 77%, respectively. The AMFM is an objective quantitative method that can be adapted for successful discrimination of multiple parenchymal lung diseases.

Diagnosis, Computer-Assisted↗

PubMed1999

Computer recognition of regional lung disease patterns.

We have developed an objective, reproducible, and automated means for the regional evaluation of the pulmonary parenchyma from computed tomography (CT) scans. This method, known as the Adaptive Multiple Feature Method (AMFM) assesses as many as 22 independent texture features in order to classify a tissue pattern. In this study, the six tissue patterns characterized were: honeycombing, ground glass, bronchovascular, nodular, emphysemalike, and normal. The lung slices were evaluated regionally using 31 x 31 pixel regions of interest. In each region of interest, an optimal subset of texture features was evaluated to determine which of the six patterns the region could be characterized as. The computer output was validated against experienced observers in three settings. In the first two readings, when the observers were blinded to the primary diagnosis of the subject, the average computer versus observer agreement was 44.4 +/- 8.7% and 47.3 +/- 9.0%, respectively. The average interobserver agreement for the same two readings were 48.8 +/- 9.1% and 52.2 +/- 10.0%, respectively. In the third reading, when the observers were provided the primary diagnosis, the average computer versus observer agreement was 51.7 +/- 2.9% where as the average interobserver agreement was 53.9 +/- 6.2%. The kappa statistic of agreement between the regions, for which the majority of the observers agreed on a pattern type, versus the computer was found to be 0.62. For regional tissue characterization, the AMFM is 100% reproducible and performs as well as experienced human observers who have been told the patient diagnosis.

Diagnosis, Computer-Assisted↗

PubMed1998

Volume-preserving smoothing of three-dimensional surfaces: application to intravascular ultrasound.

A volume-preserving three-dimensional smoothing approach is described that can be directly applied to 3D medical image data consisting of sets of 2D image slices, e.g., segmented intravascular ultrasound image sequences. Two local smoothing filters &Fscr; and &Gscr; were designed according to different smoothing goals and their performance was compared. Filtering with the &Fscr; filter of a relatively large frequency window keeps the important local characteristics of the object and results in little shrinkage while removing noise. Filtering with the Gaussian filter G that has an added volume compensation step results in no global shrinkage and may be used for multiscale filtering. The two filters can be easily extended to n-dimensional filtering.

Biomedical Engineering↗

PubMed1998

Semiautomated segmentation of ovarian follicular ultrasound images using a knowledge-based algorithm.

The application of a knowledge-based segmentation method to the problem of automatically detecting the outer follicle wall boundary in ultrasonographic images of ovaries is presented. A combination of computer detection and interactive adjustment was used to define an approximate inner follicle-wall boundary, which was then used by the computer algorithm as a priori knowledge to automatically find the outer follicle-wall border. The segmentation algorithm was tested on ultrasonographic images of women's ovaries that were imaged in vivo. The semiautomatic segmentations were compared to segmentations by an expert human observer in terms of border placement differences and in terms of quantitative parameters relevant to the physiologic status of the follicles. These physiological parameters include total and specific signal intensity from the follicle and from the follicle wall. The computer-detected outer follicle wall boundaries correlated well with the human observer-defined wall boundaries, in terms of enclosed follicle area, specific and total follicle signal, enclosed wall area, and specific and total wall signal. The actual border placement differences were also small, with a maximum placement difference of 1.47 +/- 0.83 mm and a root mean square (r.m.s.) placement difference of 0.59 +/- 0.28 mm.

Algorithms↗

PubMed1998

Intracardiac echocardiography: computerized detection of left ventricular borders.

A semi-automated method for two- and three-dimensional analysis of intracardiac echocardiography (ICE) images and image sequences is reported based on detection of epicardial and endocardial borders using graph searching. The border detection method was applied to 50 ICE images acquired in vivo in five dogs and to 108 images in 16 volumetric ICE image sequences from eight cadaveric pig hearts. The ICE images from the in vivo study showed good correlation between computer-detected and observer-defined left ventricular (LV) cavity areas and epicardial areas (r = 0.99, y = 0.98x + 0.43 [cm2]; r = 0.99, y = 0.98x + 1.11 [cm2]; respectively). In the cadaveric hearts, the LV volumes were determined with the volume measurement error of 7.6 +/- 7.7% and 11.3 +/- 11.2% for the aortic valve and mitral valve image sequences, respectively. Our method facilitates an accurate and computationally efficient approach for the quantitative assessment of ICE image data in 2D and 3D.

Animals↗

PubMed1998

Segmentation of intrathoracic airway trees: a fuzzy logic approach.

Three-dimensional (3-D) analysis of airway trees extracted from computed tomography (CT) image data can provide objective information about lung structure and function. However, manual analysis of 3-D lung CT images is tedious, time consuming and, thus, impractical for routine clinical care. We have previously reported an automated rule-based method for extraction of airway trees from 3-D CT images using a priori knowledge about airway-tree anatomy. Although the method's sensitivity was quite good, its specificity suffered from a large number of falsely detected airways. We present a new approach to airway-tree detection based on fuzzy logic that increases the method's specificity without compromising its sensitivity. The method was validated in 32 CT image slices randomly selected from five volumetric canine electron-beam CT data sets. The fuzzy-logic method significantly outperformed the previously reported rule-based method (p < 0.002).

Animals↗

PubMed1998

Tissue characterization in intravascular ultrasound images.

Intravascular ultrasound (IVUS) imaging permits direct visualization of vascular pathology. It has been used to evaluate lumen and plaque in coronary arteries and its clinical significance for guidance of coronary interventions is increasingly recognized. Conventional manual evaluation is tedious and time-consuming. This paper describes a highly automated approach to segmentation of coronary wall and plaque, and determination of plaque composition in individual IVUS images and pullback image sequences. The determined regions of plaque were classified in one of three classes: soft plaque, hard plaque, or hard plaque shadow. The method's performance was assessed in vitro and in vivo in comparison with observer-defined independent standards. In the analyzed images and image sequences, the mean border positioning error of the wall and plaque borders ranged from 0.13-0.17 mm. Plaque classification correctness was 90%.

Algorithms↗

PubMed1998

Ovarian ultrasound image analysis: follicle segmentation.

Ovarian ultrasound is an effective tool in infertility treatment. Repeated measurements of the size and shape of follicles over several days are the primary means of evaluation by physicians. Currently, follicle wall segmentation is achieved by manual tracing which is time consuming and susceptible to inter-operator variation. An automated method for follicle wall segmentation is reported that uses a four-step process based on watershed segmentation and knowledge-based graph search algorithm which utilizes priori information about follicle structure for inner and outer wall detection. The automated technique was tested on 36 ultrasonographic images of women's ovaries. Validation against manually traced borders has shown good correlation of manually defined and computer-determined area measurements (R2 = 0.85 - 0.96). The border positioning errors were small: 0.63+/-0.36 mm for inner border and 0.67+/-0.41 mm for outer border detection. The use of watershed segmentation and graph search methods facilitates fast, accurate inner and outer border detection with minimal user-interaction.

Algorithms↗

PubMed1998

Segmentation and interpretation of MR brain images: an improved active shape model.

This paper reports a novel method for fully automated segmentation that is based on description of shape and its variation using point distribution models (PDM's). An improvement of the active shape procedure introduced by Cootes and Taylor to find new examples of previously learned shapes using PDM's is presented. The new method for segmentation and interpretation of deep neuroanatomic structures such as thalamus, putamen, ventricular system, etc. incorporates a priori knowledge about shapes of the neuroanatomic structures to provide their robust segmentation and labeling in magnetic resonance (MR) brain images. The method was trained in eight MR brain images and tested in 19 brain images by comparison to observer-defined independent standards. Neuroanatomic structures in all testing images were successfully identified. Computer-identified and observer-defined neuroanatomic structures agreed well. The average labeling error was 7%+/-3%. Border positioning errors were quite small, with the average border positioning error of 0.8+/-0.1 pixels in 256 x 256 MR images. The presented method was specifically developed for segmentation of neuroanatomic structures in MR brain images. However, it is generally applicable to virtually any task involving deformable shape analysis.

Algorithms↗

PubMed1997

Towards a geometrically correct 3-D reconstruction of tortuous coronary arteries based on biplane angiography and intravascular ultrasound.

At present, 3-D reconstructions of coronary vessels are generated from intravascular ultrasound (IVUS) by stacking up ECG-gated segmented IVUS frames of a pullback sequence. This simplified approach always results in straight vessel reconstructions and, therefore, gives an incorrect representation of tortuous coronary arteries. A more realistic reconstruction of tortuous vessels may be obtained by data fusion with biplane angiography. The 3-D course of the vessel is first derived from the angiograms and then combined with the segmented IVUS images. In this paper, we focus on two problems associated with the data fusion method: The definition of the pullback path and the estimation of the IVUS catheter twist during pullback. A robust algorithm for calculation of tortuosity-induced catheter twist is reported that is based on sequential triangulation of the 3-D pullback path. The method is analyzed with computer simulations and validated in helical vessel phantoms. A largely automated data fusion approach is proposed and applied to tortuous coronary arteries in cadaveric pig hearts.

Animals↗

PubMed1997

Adaptive approach to accurate analysis of small-diameter vessels in cineangiograms.

In coronary vessels smaller than 1 mm in diameter, it is difficult to accurately identify lumen borders using existing border detection techniques. Computer-detected diameters of small coronary vessels are often severely overestimated due to the influence of the imaging system point spread function and the use of an edge operator designed for a broad range of vessel sizes, Computer-detected diameters may be corrected if a calibration curve for the X-ray system is available. Unfortunately, the performance of this postprocessing diameter correction approach is severely limited by the presence of image noise. We report here a new approach that uses a two-stage adaption of edge operator parameters to optimally match the edge operator to the local lumen diameter. In the first stage, approximate lumen diameters are detected using a single edge operator in a half-resolution image. Depending on the approximate lumen size, one of three edge operators is selected for the second full-resolution stage in which left and right coronary borders are simultaneously identified. The method was tested in a set of 72 segments of nine angiographic phantom vessels with diameters ranging from 0.46 to 4.14 mm and in 82 clinical coronary angiograms. Performance of the adaptive simultaneous border detection method was compared to that of a conventional border detection method and to that of a postprocessing diameter correction border detection method. Adaptive border detection yielded significantly improved accuracy in small phantom vessels and across all vessel sizes in comparison to the conventional and postprocessing diameter correction methods (p < 0.001 in all cases). Adaptive simultaneous coronary border detection provides both accurate and robust quantitative analysis of coronary vessels of all sizes.

Algorithms↗

PubMed1997

Quantification of pulmonary emphysema from lung computed tomography images.

A texture-based adaptive multiple feature method (AMFM) for evaluating pulmonary parenchyma from computed tomography (CT) images is described. This method incorporates multiple statistical and fractal texture features. The AMFM was compared to two previously published methods, namely, mean lung density (MLD) and the lowest fifth percentile of the histogram (HIST). First, the ability of these methods to detect subtle differences in ventral-dorsal lung density gradient in the prone normal lung was studied. Second, their abilities to differentiate between normal and emphysematous whole lung slices were compared. Finally, regional analyses comparing normal and emphysematous regions were performed by dividing the lungs. In the CT slices into six equal regions, ventral to dorsal, and analyzing each region separately. The results demonstrated that the AMFM could separate the ventral from the dorsal one-third of the normal prone lung with 89.8% accuracy, compared to an accuracy of 74.6% with the MLD and 64.4% with the HIST methods. The normal and emphysematous slices were separated on a global basis with 100.0% accuracy using the AMFM as compared to an accuracy of 94.7% and 97.4% using the MLD and HIST methods, respectively. The regional normal and emphysematous tissues were discriminated with an average accuracy of 97.9%, 89.9%, and 99.1% with the AMFM, MLD, and HIST methods, respectively. The three methods and the pulmonary function tests in the normal and emphysema groups were poorly correlated. Quantitative texture analysis using adaptive multiple features holds promise for the objective noninvasive evaluation of the pulmonary parenchyma.

Humans↗