Biomedical subjects

Jari P Kaipio

Publications and source records attributed to Jari P Kaipio.

15 recordsLinked to original sources

PubMed2006

Determination of heterogeneous thermal parameters using ultrasound induced heating and MR thermal mapping.

In this paper, a method for the determination of spatially varying thermal conductivity and perfusion coefficients of tissue is proposed. The temperature evolution in tissue is modelled with the Pennes bioheat equation. The main motivation here is a model-based optimal control for ultrasound surgery, in which the tissue properties are needed when the treatment is planned. The overview of the method is as follows. The same ultrasound transducers, which are eventually used for the treatment, are used to inflict small temperature changes in tissue. This temperature evolution is monitored using MR thermal imaging, and the tissue properties are then estimated on the basis of these measurements. Furthermore, an approach to choose transducer excitations for the determination procedure is also considered. The purpose of this paper is to introduce a method and therefore simulations are used to verify the method. Furthermore, computations are accomplished in a 2D spatial domain.

Body Temperature↗

PubMed2006

Parallelized Bayesian inversion for three-dimensional dental X-ray imaging.

Diagnostic and operational tasks based on dental radiology often require three-dimensional (3-D) information that is not available in a single X-ray projection image. Comprehensive 3-D information about tissues can be obtained by computerized tomography (CT) imaging. However, in dental imaging a conventional CT scan may not be available or practical because of high radiation dose, low-resolution or the cost of the CT scanner equipment. In this paper, we consider a novel type of 3-D imaging modality for dental radiology. We consider situations in which projection images of the teeth are taken from a few sparsely distributed projection directions using the dentist's regular (digital) X-ray equipment and the 3-D X-ray attenuation function is reconstructed. A complication in these experiments is that the reconstruction of the 3-D structure based on a few projection images becomes an ill-posed inverse problem. Bayesian inversion is a well suited framework for reconstruction from such incomplete data. In Bayesian inversion, the ill-posed reconstruction problem is formulated in a well-posed probabilistic form in which a priori information is used to compensate for the incomplete information of the projection data. In this paper we propose a Bayesian method for 3-D reconstruction in dental radiology. The method is partially based on Kolehmainen et al. 2003. The prior model for dental structures consist of a weighted l1 and total variation (TV)-prior together with the positivity prior. The inverse problem is stated as finding the maximum a posteriori (MAP) estimate. To make the 3-D reconstruction computationally feasible, a parallelized version of an optimization algorithm is implemented for a Beowulf cluster computer. The method is tested with projection data from dental specimens and patient data. Tomosynthetic reconstructions are given as reference for the proposed method.

Algorithms↗

PubMed2005

Dynamic physiological modeling for functional diffuse optical tomography.

Diffuse optical tomography (DOT) is a noninvasive imaging technology that is sensitive to local concentration changes in oxy- and deoxyhemoglobin. When applied to functional neuroimaging, DOT measures hemodynamics in the scalp and brain that reflect competing metabolic demands and cardiovascular dynamics. The diffuse nature of near-infrared photon migration in tissue and the multitude of physiological systems that affect hemodynamics motivate the use of anatomical and physiological models to improve estimates of the functional hemodynamic response. In this paper, we present a linear state-space model for DOT analysis that models the physiological fluctuations present in the data with either static or dynamic estimation. We demonstrate the approach by using auxiliary measurements of blood pressure variability and heart rate variability as inputs to model the background physiology in DOT data. We evaluate the improvements accorded by modeling this physiology on ten human subjects with simulated functional hemodynamic responses added to the baseline physiology. Adding physiological modeling with a static estimator significantly improved estimates of the simulated functional response, and further significant improvements were achieved with a dynamic Kalman filter estimator (paired t tests, n=10, P<0.05). These results suggest that physiological modeling can improve DOT analysis. The further improvement with the Kalman filter encourages continued research into dynamic linear modeling of the physiology present in DOT. Cardiovascular dynamics also affect the blood-oxygen-dependent (BOLD) signal in functional magnetic resonance imaging (fMRI). This state-space approach to DOT analysis could be extended to BOLD fMRI analysis, multimodal studies and real-time analysis.

Blood Pressure↗

PubMed2005

Coupled radiative transfer equation and diffusion approximation model for photon migration in turbid medium with low-scattering and non-scattering regions.

In this paper, a coupled radiative transfer equation and diffusion approximation model is extended for light propagation in turbid medium with low-scattering and non-scattering regions. The light propagation is modelled with the radiative transfer equation in sub-domains in which the assumptions of the diffusion approximation are not valid. The diffusion approximation is used elsewhere in the domain. The two equations are coupled through their boundary conditions and they are solved simultaneously using the finite element method. The streamline diffusion modification is used to avoid the ray-effect problem in the finite element solution of the radiative transfer equation. The proposed method is tested with simulations. The results of the coupled model are compared with the finite element solutions of the radiative transfer equation and the diffusion approximation and with results of Monte Carlo simulation. The results show that the coupled model can be used to describe photon migration in turbid medium with low-scattering and non-scattering regions more accurately than the conventional diffusion model.

Animals↗

PubMed2005

Scanning path optimization for ultrasound surgery.

One of the problems in ultrasound surgery is the long treatment times when large tumour volumes are sonicated. Large tumours are usually treated by scanning the tumour volume using a sequence of individual focus points. During the scanning, it is possible that surrounding healthy tissue suffers from undesired temperature rise. The selection of the scanning path so that the tumour volume is treated as fast as possible while temperature rise in healthy tissue is minimized would increase the efficiency of ultrasound surgery. The main purpose of this paper is to develop a computationally efficient method which optimizes the scanning path. The optimization algorithm is based on the minimum time formulation of the optimal control theory. The developed algorithm uses quadratic cost criteria to obtain the desired thermal dose in the tumour region. The derived method is evaluated with numerical simulations in 3D which are applied to ultrasound surgery of the breast in simplified geometry. Results from the simulations show that the treatment time as well as the total applied energy can be decreased from 16% to 43% as compared to standard sonication. The robustness of the optimized scanning path is studied by varying the perfusion and absorption in the tumour region.

Body Temperature↗

PubMed2005

Computational calibration method for optical tomography.

We propose a computational calibration method for optical tomography. The model of the calibration scheme is based on the rotation symmetry of source and detector positions in the measurement setup. The relative amplitude losses and phase shifts at the optic fibers are modeled by complex-valued coupling coefficients. The coupling coefficients can be estimated when optical tomography data from a homogeneous and isotropic object are given. Once these coupling coefficients have been estimated, any data measured with the same measurement setup can be corrected for the relative variation in the data due to source and detector losses. The final calibration of the data for the source and detector losses and the source calibration between the data and the forward model are obtained as part of the initial estimation for reconstruction. The calibration method was tested with simulations and measurements. The results show that the coupling coefficients of the sources and detectors can be estimated with good accuracy. Furthermore, the results show that the method can significantly improve the quality of reconstructed images.

Algorithms↗

PubMed2005

Hybrid radiative-transfer-diffusion model for optical tomography.

A hybrid radiative-transfer-diffusion model for optical tomography is proposed. The light propagation is modeled with the radiative-transfer equation in the vicinity of the laser sources, and the diffusion approximation is used elsewhere in the domain. The solution of the radiative-transfer equation is used to construct a Dirichlet boundary condition for the diffusion approximation on a fictitious interface within the object. This boundary condition constitutes an approximative distributed source model for the diffusion approximation in the remaining area. The results from the proposed approach are compared with finite-element solutions of the radiative-transfer equation and the diffusion approximation and Monte Carlo simulation. The results show that the method improves the accuracy of the forward model compared with the conventional diffusion model.

Computer Simulation↗

PubMed2005

Physiological system identification with the Kalman filter in diffuse optical tomography.

Algorithms↗

PubMed2005

A full-wave Helmholtz model for continuous-wave ultrasound transmission.

A full-wave Helmholtz model of continuous-wave (CW) ultrasound fields may offer several attractive features over widely used partial-wave approximations. For example, many full-wave techniques can be easily adjusted for complex geometries, and multiple reflections of sound are automatically taken into account in the model. To date, however, the full-wave modeling of CW fields in general 3D geometries has been avoided due to the large computational cost associated with the numerical approximation of the Helmholtz equation. Recent developments in computing capacity together with improvements in finite element type modeling techniques are making possible wave simulations in 3D geometries which reach over tens of wavelengths. The aim of this study is to investigate the feasibility of a full-wave solution of the 3D Helmholtz equation for modeling of continuous-wave ultrasound fields in an inhomogeneous medium. The numerical approximation of the Helmholtz equation is computed using the ultraweak variational formulation (UWVF) method. In addition, an inverse problem technique is utilized to reconstruct the velocity distribution on the transducer which is used to model the sound source in the UWVF scheme. The modeling method is verified by comparing simulated and measured fields in the case of transmission of 531 kHz CW fields through layered plastic plates. The comparison shows a reasonable agreement between simulations and measurements at low angles of incidence but, due to mode conversion, the Helmholtz model becomes insufficient for simulating ultrasound fields in plates at large angles of incidence.

Algorithms↗

PubMed2004

Simulation study for thermal dose optimization in ultrasound surgery of the breast.

In this paper the previously published optimization algorithm for thermal dose optimization is tested with numerical simulations. The simulations concern the thermal dose optimization in ultrasound surgery of the breast. The optimization algorithm is extended by setting the inequality constraint approximations to temperature in healthy tissue as well as in tumor region. In addition, the simulations are accomplished in realistic 3D geometry with varying thermal parameters. Another topic of the paper is to show the potential of the hemispherical phased array applicator for ultrasound surgery of the breast. With such an applicator larger tissue volumes can be treated with shorter time as compared to single element transducers. In simulations the geometrical focus of the applicator was placed mechanically in the middle of the treatable region. The whole tumor region was then scanned electrically by changing the phase of the emitted wave from individual elements. The simulations indicate that a feasible treatment plan can be achieved. In simulated cases the desired thermal dose was achieved for tumors with diameter from 1.5 to 2.4 cm, depending on the position of tumor. The maximum temperature limitations of 45 degrees C in healthy region and 80 degrees C in tumor region can be maintained in all simulations.

Algorithms↗

PubMed2004

Theoretical analysis of the influence of aerosol size distribution and physical activity on particle deposition pattern in human lungs.

OBJECTIVES: A theoretical comparison of modeled particle depositions in the human respiratory tract was performed by taking into account different particle number and mass size distributions and physical activity in an urban environment. METHODS: Urban-air data on particulate concentrations in the size range 10 nm-10 microm were used to estimate the hourly average particle number and mass size distribution functions. The functions were then combined with the deposition probability functions obtained from a computerized ICRP 66 deposition model of the International Commission on Radiological Protection to calculate the numbers and masses of particles deposited in five regions of the respiratory tract of a male adult. The man's physical activity and minute ventilation during the day were taken into account in the calculations. RESULTS: Two different mass and number size distributions of aerosol particles with equal (computed) <10 microm particle mass concentrations gave clearly different deposition patterns in the central and peripheral regions of the human respiratory tract. The deposited particle numbers and masses were much higher during the day (0700-1900) than during the night (1900-0700) because an increase in physical activity and ventilation were temporally associated with highly increased traffic-derived particles in urban outdoor air. CONCLUSIONS: In future analyses of the short-term associations between particulate air pollution and health, it would not only be important to take into account the outdoor-to-indoor penetration of different particle sizes and human time-activity patterns, but also actual lung deposition patterns and physical activity in significant microenvironments.

Activities of Daily Living↗

PubMed2003

Time-series estimation of biological factors in optical diffusion tomography.

We apply state space estimation techniques to the time-varying reconstruction problem in optical tomography. We develop a stochastic model for describing the evolution of quasi-sinusoidal medical signals such as the heartbeat, assuming these are represented as a known frequency with randomly varying amplitude and phase. We use the extended Kalman filter in combination with spatial regularization techniques to reconstruct images from highly under-determined time-series data. This system also naturally segments activity belonging to different biological processes. We present reconstructions of simulated data and of real data recorded from the human motor cortex (Franceschini et al 2000 Optics Express 6 49-57). It is argued that the application of these time-series techniques improves both the fidelity and temporal resolution of reconstruction in optical tomography.

Algorithms↗

PubMed2003

Thermal dose optimization method for ultrasound surgery.

In this paper, a model-based optimization method is derived to control the thermal dose in biological tissues for ultrasound surgery. The optimization method uses the bioheat equation as a system model and quadratic cost criteria for the desired thermal dose. Time-harmonic quasi-stationary ultrasound fields are used as the heat source. In this method the optimal phase and the amplitude trajectories are found directly by minimizing the associated cost function. The approach also allows for maximum input amplitude constraints. The method is based on the Hamiltonian form of the system and results in a large dimensional nonlinear optimization problem which is solved with a gradient-type iterative scheme. The performance of the optimization method is tested with 2D simulations and it is shown that the approach is able to yield a feasible nominal solution. This nominal evolution would then eventually be sought to be maintained with the help of a feedback controller during the actual sonication.

Algorithms↗

PubMed2003

Modeling of anomalies due to hydrophones in continuous-wave ultrasound fields.

Needle and spot-poled membrane hydrophones using polyvinylidene fluoride (PVDF) sensors are widely used for characterization of biomedical ultrasound fields. It is known that, in measurements of continuous-wave (CW) fields, standing waves may be generated between the transducer and the hydrophone, distorting the field and possibly alternating the signal of the hydrophone. This study uses a three-dimensional, full-wave method to computationally simulate the distortion in the CW field caused by needle and membrane hydrophones. The physical model used in simulations is based on the linear time-harmonic wave equation, which therefore neglects the effects of nonlinear wave propagation. The significance of the distortion is examined by comparing fields emitted by 0.5-5.0 MHz planar circular transducers in the absence and presence of the hydrophones. In addition, the effect of the field distortions on the signal of the hydrophones is studied with simulated measurements. The simulations showed an observable standing wave pattern between the source and the needle hydrophone if the diameter of the needle was larger than a half of the wavelength. However, the standing waves had no clear effect on the signal of the hydrophone. The presence of membrane hydrophone in the CW field generated notable standing waves. Furthermore, the standing waves caused a periodic distortion to the signal of the membrane hydrophone.

Artifacts↗

PubMed2003

State-estimation approach to the nonstationary optical tomography problem.

We propose a new numerical approach to the nonstationary optical (diffusion) tomography (OT) problem. The assumption in the method is that the absorption and/or diffusion coefficients are nonstationary in the sense that they may exhibit significant changes during the time that is needed to measure data for one traditional image frame. In the proposed method, the OT problem is formulated as a state-estimation problem. Within the state-estimation formulation, the absorption and/or diffusion coefficients are considered a stochastic process. The objective is to estimate a sequence of states for the process when the state evolution model for the process, the observation model for OT experiments, and data on the exterior boundary are given. In the proposed method, the state estimates are computed by using Kalman filtering techniques. The performance of the proposed method is evaluated on the basis of synthetic data. The simulations also illustrate that further improvements to the results in nonstationary applications can be obtained by adjustment of the measurement protocol.

Models, Theoretical↗