Radovan Jirik - Academia.edu (original) (raw)

Papers by Radovan Jirik

Technology and Health Care, Jul 1, 2004

Perfusion imaging is an important diagnostic tool used mostly in oncology, neurology and cardiolo... more Perfusion imaging is an important diagnostic tool used mostly in oncology, neurology and cardiology, to assess the perfusion status of the tissue on a capillary level, e.g. assessment of angiogenesis, ischemic regions and inflammation. This contribution is a review of recent advances in dynamic contrast-enhanced magnetic-resonance and ultrasound imaging.

In recent years, several studies comparing ASL vs. DCE-MRI appeared due to an expansion of ASL fr... more In recent years, several studies comparing ASL vs. DCE-MRI appeared due to an expansion of ASL from brain applications also to other organs (e.g. pulmonary parenchyma(1), tumour(2)). These studies indirectly compared blood flow (Fb) estimated with ASL to the perfusion parameters estimated by DCE-MRI which are only related to Fb but not equivalent. Our DCE-MRI method3 is based on the ATH pharmacokinetic model(4) providing estimates of Fb. This provides a direct comparison of the same quantity estimated using ASL and DCE-MRI. Compared to previous approaches aiming at replacement of one method by another, this study aims to prepare their combination and to provide more reliable perfusion-parameter estimate.

Magnetic Resonance Imaging, 2021

PURPOSE The composite vascular transport function of a brain voxel consists of one convolutional ... more PURPOSE The composite vascular transport function of a brain voxel consists of one convolutional component for the arteries, one for the capillaries and one for the veins in the voxel of interest. Here, the goal is to find each of these three convolutional components and the associated arterial input function. PHARMACOKINETIC MODELLING The single voxel vascular transport functions for arteries, capillaries and veins were all modelled as causal exponential functions. Each observed multipass tissue contrast function was as a first approximation modelled as the resulting parametric composite vascular transport function convolved with a nonparametric and voxel specific multipass arterial input function. Subsequently, the residue function was used in the true perfusion equation to optimize the three parameters of the exponential functions. DECONVOLUTION METHODS For each voxel, the parameters of the three exponential functions were estimated by successive iterative blind deconvolutions using versions of the Lucy-Richardson algorithm. The final multipass arterial input function was then computed by nonblind deconvolution using the Lucy-Richardson algorithm and the estimated composite vascular transport function. RESULTS Simulations showed that the algorithm worked. The estimated mean transit time of arteries, capillaries and veins of the simulated data agreed with the known input values. For real data, the estimated capillary mean transit times agreed with known values for this parameter. The nonparametric multipass arterial input functions were used to derive the associated map of the arrival time. The arrival time map of a healthy volunteer agreed with known arterial anatomy and physiology. CONCLUSION Clinically important new voxelwise hemodynamic information for arteries, capillaries and veins separately can be estimated using multipass tissue contrast functions and the iterative blind Lucy-Richardson deconvolution algorithm.

USCT-sim is a fast simulation tool for ultrasound transmission tomography systems. It is written ... more USCT-sim is a fast simulation tool for ultrasound transmission tomography systems. It is written in Matlab and based on following approximations: * Discretization of the simulated volume -- the volume describing the shape and material properties of the depicted phantom is discretized into regular voxels (cubes) representing areas with homogeneous material properties. * Straight propagation -- the ultrasonic pulses are modeled along straight line between sending and receiving transducer assuming a spherical wave. * Transducer characteristics -- the shape and size of the transducers is neglected in the simulation, however the effects the heterogeneous radiation characteristic of the transducers can be defined by the user as a function of angle-dependent frequency response. * Scattering effects -- to simulate the reflection/scattering effects the volume is filled with large number of scattering points and the propagation of the ultrasonic pulse is computed for the first-order scattering paths (sender-scatterer-receiver).

ISMRM Annual Meeting

We propose to combine DCE and DSC-MRI in a simultaneous acquisition and processing scheme to prov... more We propose to combine DCE and DSC-MRI in a simultaneous acquisition and processing scheme to provide more information for estimation of the arterial input function using multi-channel blind deconvolution. On simulated and flow-phantom data, we show that DCE-DSC blind deconvolution is superior to standard DCE blind deconvolution, especially for low signal-to-noise-ratio conditions.

This work is focused on estimation of an arterial input function (AIF) in DCE-MRI. We propose a n... more This work is focused on estimation of an arterial input function (AIF) in DCE-MRI. We propose a new concept of blind deconvolution to use as much available information as possible. In contrast to multi-channel blind deconvolution based on processing of selected tissue signals, our all-channel blind deconvolution uses tissue signals of all voxels within the studied tissue to simultaneously estimate the AIF and perfusion maps. In addition, edge-preserving spatial regularization is included in the perfusion-map estimation scheme. The method is illustrated on DCE-MRI recordings of tumor-bearing mice.

In DCE-MRI, tissue contrast-agent (CA) concentration curves are modeled as a convolution of the a... more In DCE-MRI, tissue contrast-agent (CA) concentration curves are modeled as a convolution of the arterial input function (AIF) and the impulse residue function (IRF). The 2CXM and ATH models [1] are the most widely used advanced IRF models that provide separate estimates of blood flow, Fb, and permeability- surface area product, PS, contrary to the commonly applied Tofts models. No consensus exists on which advanced pharmacokinetic model is better. Simulation-based and blind-deconvolution-based preclinical model comparisons are published. This contribution presents a new model-evaluation method based on high- and low-molecular weight (MW) contrast-agents administered within one examination. Some perfusion parameters are expected to be MW-independent (namely Fb and blood volume—vb), while PS should decrease with increasing MW.

Magnetic Resonance Imaging, Feb 1, 2018

Objective: An extension of single-and multi-channel blind deconvolution is presented to improve t... more Objective: An extension of single-and multi-channel blind deconvolution is presented to improve the estimation of the arterial input function (AIF) in quantitative dynamic contrast enhanced magnetic resonance imaging (DCE-MRI). Methods: The Lucy-Richardson expectation-maximization algorithm is used to obtain estimates of the AIF and the tissue residue function (TRF). In the first part of the algorithm, nonparametric estimates of the AIF and TRF are obtained. In the second part, the decaying part of the AIF is approximated by three decaying exponential functions with the same delay, giving an almost noise free semi-parametric AIF. Simultaneously, the TRF is approximated using the adiabatic approximation of the Johnson-Wilson (aaJW) pharmacokinetic model. Results: In simulations and tests on real data, use of this AIF gave perfusion values close to those obtained with the corresponding previously published nonparametric AIF, and are more noise robust. Conclusion: When used subsequently in voxelwise perfusion analysis, these semi-parametric AIFs should give more correct perfusion analysis maps less

Proceedings of SPIE, Apr 12, 2005

The paper presents a new ultrasonic attenuation imaging method which might be used as a new imagi... more The paper presents a new ultrasonic attenuation imaging method which might be used as a new imaging modality, targeted at breast cancer diagnostics. Two approaches based on ultrasonic imaging are combined together, namely the estimation of ultrasound attenuation coefficients from pulse-echo B-mode imaging data and an ultrasound computer tomography imaging technique. A recently published method for estimation of the ultrasound attenuation coefficient using the log-spectrum analysis is applied to radiofrequency signals acquired by an ultrasound computer tomography system to estimate images of the attenuation coefficients. The examined volume (e.g. female breast) is enclosed by several thousand ultrasound transducers. Radiofrequency signals from all transducers using all sending positions are recorded. Compared to the known ultrasound attenuation tomography methods, not only the directly transmitted signal, but also the reflected and scattered signals are processed here, i.e. substantially more information is used. The method is presented in its initial stage. The applied algorithm is derived using simplifying assumptions which will be relaxed in further research. However, even at this stage the resulting attenuation image is of higher quality than the standard attenuation imaging methods applied to the same data set.

Neuro-oncology, Sep 1, 2014

Treatment of primary and recurrent glioblastoma with anti-angiogenic therapies, either alone or i... more Treatment of primary and recurrent glioblastoma with anti-angiogenic therapies, either alone or in combination with chemotherapy, fails to extend overall survival, despite the often reported improvements in progression free survival and patient health condition. To improve the efficacy of these therapies, a better understanding of the mechanisms of tumour adaptation and treatment escape is warranted, while at the same time adopting imaging protocols that evaluate tumour progression without ambiguity. The complementary roles of Magnetic Resonance Imaging and Positron Emission Tomography can help to elucidate the physiologic and metabolic changes induced by anti-angiogenic agents, and better appreciate the clinical response at early stages of the treatment. In the present study, we have used this multi-modal imaging approach to investigate the changes induced by bevacizumab in pre-clinical models of glioblastomas obtained from patient-derived biopsies. We report longitudinal changes in vascular morphology and function, and describe how the changes in blood supply lead to increased intratumoral hypoxia, resulting in high glycolytic activity and tumour invasiveness.

IEEE Transactions on Biomedical Engineering, Apr 1, 2012

Multipass dynamic MRI and pharmacokinetic modeling are used to estimate perfusion parameters of l... more Multipass dynamic MRI and pharmacokinetic modeling are used to estimate perfusion parameters of leaky capillaries. Curve fitting and nonblind deconvolution are the established methods to derive the perfusion estimates from the observed arterial input function (AIF) and tissue tracer concentration function. These nonblind methods are sensitive to errors in the AIF, measured in some nearby artery or estimated by multichannel blind deconvolution. Here, a single-channel blind deconvolution algorithm is presented, which only uses a single tissue tracer concentration function to estimate the corresponding AIF and tissue impulse response function. That way, many errors affecting these functions are reduced. The validity of the algorithm is supported by simulations and tests on real data from mouse. The corresponding nonblind and multichannel methods are also presented. Index Terms-Arterial input function (AIF), blind deconvolution, dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), multichannel, perfusion, single channel. I. INTRODUCTION D URING the last two decades, it has become possible to measure region-specific microvascular perfusion parameters by MRI. Reliable microvascular perfusion parameters of normal and pathological tissues have a large clinical impor-Manuscript

WORLD SCIENTIFIC eBooks, May 1, 2007

IFMBE proceedings, May 30, 2018

This paper introduces new variational formulation for reconstruction from subsampled dynamic cont... more This paper introduces new variational formulation for reconstruction from subsampled dynamic contrast-enhanced DCE-MRI data, that combines a data-driven approach using estimated temporal basis and total variation regularization (PCA TV). We also experimentally compares the performance of such model with two other state-of-the-art formulations. One models the shape of perfusion curves in time as a sum of a curve belonging to a low-dimensional space and a function sparse in a suitable domain (L + S model). The other possibility is to regularize both spatial and time domains (ICTGV). We are dealing with the specific situation of the DCE-MRI acquisition with a 9.4T small animal scanner, working with noisier signals than human scanners and with a smaller number of coil elements that can be used for parallel acquisition and small voxels. Evaluation of the selected methods is done through subsampled reconstruction of radially-sampled DCE-MRI data. Our analysis shows that compressed sensed MRI in the form of regularization can be used to increase the temporal resolution of acquisition while keeping a sufficient signal-to-noise ratio.

This paper is focused on quantitative perfusion analysis using pulsed ASL (FAIR-RARE) and DCE-MRI... more This paper is focused on quantitative perfusion analysis using pulsed ASL (FAIR-RARE) and DCE-MRI (using high-and low-molecular-weight contrast agents) in a mouse tumour model. Tumour blood-flow maps of both methods were compared using visual assessment, region analysis (median, percentiles), scatter plots and correlation coefficients. ASL blood-flow estimates matched the DCE-MRI blood-flow estimations in some cases. Possible reasons for poor match in the other cases were investigated. This study indicates that in tumour perfusion analysis, we might profit from the combination of ASL and DCE-MRI instead of using just one of them.

Magma, 2016

In vivo T(1) mapping of rat myocardium can be challenging given to the high heart and respiratory... more In vivo T(1) mapping of rat myocardium can be challenging given to the high heart and respiratory rate and small size of the heart. We propose a new method for T1 estimation based on retrospectively gated inversion-recovery fast low-angle shot (IR FLASH) pulse sequence. The method was applied and validated in a doxorubicin study.

In vivo diffusion tensor imaging (DTI) of rat thoracic spinal cord was performed on five healthy ... more In vivo diffusion tensor imaging (DTI) of rat thoracic spinal cord was performed on five healthy rats. Axial diffusion images were obtained using a standard spin echo diffusion weighted sequence. The fractional anisotropy (FA), longitudinal (LD) and transverse (TD) diffusivities and the mean diffusivity were estimated. Differences in these parameters between white and grey matter were in accord with theory and in the range reported in literature.

The aim of this study was to investigate Mag 102-6, a maghemite hybrid drug nanocarrier, as a pot... more The aim of this study was to investigate Mag 102-6, a maghemite hybrid drug nanocarrier, as a potential T 2 contrast agent (CA) for magnetic resonance imaging (MRI). Samples of agar gel mixed with different Fe concentrations of Mag 102-6 were measured at laboratory temperature for relaxivity r 2 determination in 9.4 T. The results were compared with commercial CA FeraSpin XXL measured in the same arrangement. In addition, the r 2 of Mag 102-6 in saline solution at physiological temperature 37.7°C was measured. MRI was performed with four mice using a 9.4T NMR scanner before, and up to 24 h post-injection (p.i.) of Mag 102-6 (dose 5 mg Fe kg-1). Images of abdomen were continuously acquired by segmented Multi Gradient Echo (MGE) pulse sequence from 1 minute before the CA application to 20 minutes p.i. The T 1-weighted (T 1-w) and T 2-weighted (T 2-w) images were captured before the application and 25 minutes, 3.5, 7 and 24 hours after CA application. R 2 * changes in time were estimated from MGE images for various anatomical regions (kidney, muscles, liver) by fitting of signal intensities. Mag 102-6 and FeraSpin XXL had comparable r 2 values. Mag 102-6 showed the potential to be monitored by MRI as a T 2 CA.

IFMBE proceedings, May 30, 2018

Dynamic contrast-enhanced magnetic resonance imaging obtains information about tissue perfusion a... more Dynamic contrast-enhanced magnetic resonance imaging obtains information about tissue perfusion and permeability. Following the administration of a contrast agent, concentration-time curves measured in each voxel are fitted by a pharmacokinetic model formulated as a time-domain convolution of an arterial input function (AIF) and an impulse residue function (IRF). Since the measurement window contains hundreds of time samples, the discrete convolution is demanding, even when it is performed via discrete Fourier transform (DFT). Additionally, its discretization causes convergence complications in the curve fitting and it is not applicable to functions without a closed-form expression in the time domain, e.g. tissue homogeneity model IRF. Both issues can be solved by formulating the functions in a closed form in the Fourier domain. In the Fourier domain, the model transforms to multiplication of IRF and AIF, followed by the inverse DFT. To avoid time-domain aliasing, the number of samples in the Fourier domain must be higher than the sum of supports of the functions in the time domain. If the functions are slowly decaying exponentials, the support is theoretically infinite, which dramatically reduces the computational performance. In this contribution, we propose a modification of IRF in the Fourier domain to consider the measurement window. Our solution reduces the required number of samples to three times the measurement window compared to dozens needed without the modification and reduces the number of DFTs. This provides faster evaluation of the pharmacokinetic model and its derivatives for each voxel in each iteration of the curve fitting.

Technology and Health Care, Jul 1, 2004

Perfusion imaging is an important diagnostic tool used mostly in oncology, neurology and cardiolo... more Perfusion imaging is an important diagnostic tool used mostly in oncology, neurology and cardiology, to assess the perfusion status of the tissue on a capillary level, e.g. assessment of angiogenesis, ischemic regions and inflammation. This contribution is a review of recent advances in dynamic contrast-enhanced magnetic-resonance and ultrasound imaging.

In recent years, several studies comparing ASL vs. DCE-MRI appeared due to an expansion of ASL fr... more In recent years, several studies comparing ASL vs. DCE-MRI appeared due to an expansion of ASL from brain applications also to other organs (e.g. pulmonary parenchyma(1), tumour(2)). These studies indirectly compared blood flow (Fb) estimated with ASL to the perfusion parameters estimated by DCE-MRI which are only related to Fb but not equivalent. Our DCE-MRI method3 is based on the ATH pharmacokinetic model(4) providing estimates of Fb. This provides a direct comparison of the same quantity estimated using ASL and DCE-MRI. Compared to previous approaches aiming at replacement of one method by another, this study aims to prepare their combination and to provide more reliable perfusion-parameter estimate.

Magnetic Resonance Imaging, 2021

PURPOSE The composite vascular transport function of a brain voxel consists of one convolutional ... more PURPOSE The composite vascular transport function of a brain voxel consists of one convolutional component for the arteries, one for the capillaries and one for the veins in the voxel of interest. Here, the goal is to find each of these three convolutional components and the associated arterial input function. PHARMACOKINETIC MODELLING The single voxel vascular transport functions for arteries, capillaries and veins were all modelled as causal exponential functions. Each observed multipass tissue contrast function was as a first approximation modelled as the resulting parametric composite vascular transport function convolved with a nonparametric and voxel specific multipass arterial input function. Subsequently, the residue function was used in the true perfusion equation to optimize the three parameters of the exponential functions. DECONVOLUTION METHODS For each voxel, the parameters of the three exponential functions were estimated by successive iterative blind deconvolutions using versions of the Lucy-Richardson algorithm. The final multipass arterial input function was then computed by nonblind deconvolution using the Lucy-Richardson algorithm and the estimated composite vascular transport function. RESULTS Simulations showed that the algorithm worked. The estimated mean transit time of arteries, capillaries and veins of the simulated data agreed with the known input values. For real data, the estimated capillary mean transit times agreed with known values for this parameter. The nonparametric multipass arterial input functions were used to derive the associated map of the arrival time. The arrival time map of a healthy volunteer agreed with known arterial anatomy and physiology. CONCLUSION Clinically important new voxelwise hemodynamic information for arteries, capillaries and veins separately can be estimated using multipass tissue contrast functions and the iterative blind Lucy-Richardson deconvolution algorithm.

USCT-sim is a fast simulation tool for ultrasound transmission tomography systems. It is written ... more USCT-sim is a fast simulation tool for ultrasound transmission tomography systems. It is written in Matlab and based on following approximations: * Discretization of the simulated volume -- the volume describing the shape and material properties of the depicted phantom is discretized into regular voxels (cubes) representing areas with homogeneous material properties. * Straight propagation -- the ultrasonic pulses are modeled along straight line between sending and receiving transducer assuming a spherical wave. * Transducer characteristics -- the shape and size of the transducers is neglected in the simulation, however the effects the heterogeneous radiation characteristic of the transducers can be defined by the user as a function of angle-dependent frequency response. * Scattering effects -- to simulate the reflection/scattering effects the volume is filled with large number of scattering points and the propagation of the ultrasonic pulse is computed for the first-order scattering paths (sender-scatterer-receiver).

ISMRM Annual Meeting

We propose to combine DCE and DSC-MRI in a simultaneous acquisition and processing scheme to prov... more We propose to combine DCE and DSC-MRI in a simultaneous acquisition and processing scheme to provide more information for estimation of the arterial input function using multi-channel blind deconvolution. On simulated and flow-phantom data, we show that DCE-DSC blind deconvolution is superior to standard DCE blind deconvolution, especially for low signal-to-noise-ratio conditions.

This work is focused on estimation of an arterial input function (AIF) in DCE-MRI. We propose a n... more This work is focused on estimation of an arterial input function (AIF) in DCE-MRI. We propose a new concept of blind deconvolution to use as much available information as possible. In contrast to multi-channel blind deconvolution based on processing of selected tissue signals, our all-channel blind deconvolution uses tissue signals of all voxels within the studied tissue to simultaneously estimate the AIF and perfusion maps. In addition, edge-preserving spatial regularization is included in the perfusion-map estimation scheme. The method is illustrated on DCE-MRI recordings of tumor-bearing mice.

In DCE-MRI, tissue contrast-agent (CA) concentration curves are modeled as a convolution of the a... more In DCE-MRI, tissue contrast-agent (CA) concentration curves are modeled as a convolution of the arterial input function (AIF) and the impulse residue function (IRF). The 2CXM and ATH models [1] are the most widely used advanced IRF models that provide separate estimates of blood flow, Fb, and permeability- surface area product, PS, contrary to the commonly applied Tofts models. No consensus exists on which advanced pharmacokinetic model is better. Simulation-based and blind-deconvolution-based preclinical model comparisons are published. This contribution presents a new model-evaluation method based on high- and low-molecular weight (MW) contrast-agents administered within one examination. Some perfusion parameters are expected to be MW-independent (namely Fb and blood volume—vb), while PS should decrease with increasing MW.

Magnetic Resonance Imaging, Feb 1, 2018

Objective: An extension of single-and multi-channel blind deconvolution is presented to improve t... more Objective: An extension of single-and multi-channel blind deconvolution is presented to improve the estimation of the arterial input function (AIF) in quantitative dynamic contrast enhanced magnetic resonance imaging (DCE-MRI). Methods: The Lucy-Richardson expectation-maximization algorithm is used to obtain estimates of the AIF and the tissue residue function (TRF). In the first part of the algorithm, nonparametric estimates of the AIF and TRF are obtained. In the second part, the decaying part of the AIF is approximated by three decaying exponential functions with the same delay, giving an almost noise free semi-parametric AIF. Simultaneously, the TRF is approximated using the adiabatic approximation of the Johnson-Wilson (aaJW) pharmacokinetic model. Results: In simulations and tests on real data, use of this AIF gave perfusion values close to those obtained with the corresponding previously published nonparametric AIF, and are more noise robust. Conclusion: When used subsequently in voxelwise perfusion analysis, these semi-parametric AIFs should give more correct perfusion analysis maps less

Proceedings of SPIE, Apr 12, 2005

The paper presents a new ultrasonic attenuation imaging method which might be used as a new imagi... more The paper presents a new ultrasonic attenuation imaging method which might be used as a new imaging modality, targeted at breast cancer diagnostics. Two approaches based on ultrasonic imaging are combined together, namely the estimation of ultrasound attenuation coefficients from pulse-echo B-mode imaging data and an ultrasound computer tomography imaging technique. A recently published method for estimation of the ultrasound attenuation coefficient using the log-spectrum analysis is applied to radiofrequency signals acquired by an ultrasound computer tomography system to estimate images of the attenuation coefficients. The examined volume (e.g. female breast) is enclosed by several thousand ultrasound transducers. Radiofrequency signals from all transducers using all sending positions are recorded. Compared to the known ultrasound attenuation tomography methods, not only the directly transmitted signal, but also the reflected and scattered signals are processed here, i.e. substantially more information is used. The method is presented in its initial stage. The applied algorithm is derived using simplifying assumptions which will be relaxed in further research. However, even at this stage the resulting attenuation image is of higher quality than the standard attenuation imaging methods applied to the same data set.

Neuro-oncology, Sep 1, 2014

Treatment of primary and recurrent glioblastoma with anti-angiogenic therapies, either alone or i... more Treatment of primary and recurrent glioblastoma with anti-angiogenic therapies, either alone or in combination with chemotherapy, fails to extend overall survival, despite the often reported improvements in progression free survival and patient health condition. To improve the efficacy of these therapies, a better understanding of the mechanisms of tumour adaptation and treatment escape is warranted, while at the same time adopting imaging protocols that evaluate tumour progression without ambiguity. The complementary roles of Magnetic Resonance Imaging and Positron Emission Tomography can help to elucidate the physiologic and metabolic changes induced by anti-angiogenic agents, and better appreciate the clinical response at early stages of the treatment. In the present study, we have used this multi-modal imaging approach to investigate the changes induced by bevacizumab in pre-clinical models of glioblastomas obtained from patient-derived biopsies. We report longitudinal changes in vascular morphology and function, and describe how the changes in blood supply lead to increased intratumoral hypoxia, resulting in high glycolytic activity and tumour invasiveness.

IEEE Transactions on Biomedical Engineering, Apr 1, 2012

Multipass dynamic MRI and pharmacokinetic modeling are used to estimate perfusion parameters of l... more Multipass dynamic MRI and pharmacokinetic modeling are used to estimate perfusion parameters of leaky capillaries. Curve fitting and nonblind deconvolution are the established methods to derive the perfusion estimates from the observed arterial input function (AIF) and tissue tracer concentration function. These nonblind methods are sensitive to errors in the AIF, measured in some nearby artery or estimated by multichannel blind deconvolution. Here, a single-channel blind deconvolution algorithm is presented, which only uses a single tissue tracer concentration function to estimate the corresponding AIF and tissue impulse response function. That way, many errors affecting these functions are reduced. The validity of the algorithm is supported by simulations and tests on real data from mouse. The corresponding nonblind and multichannel methods are also presented. Index Terms-Arterial input function (AIF), blind deconvolution, dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), multichannel, perfusion, single channel. I. INTRODUCTION D URING the last two decades, it has become possible to measure region-specific microvascular perfusion parameters by MRI. Reliable microvascular perfusion parameters of normal and pathological tissues have a large clinical impor-Manuscript

WORLD SCIENTIFIC eBooks, May 1, 2007

IFMBE proceedings, May 30, 2018

This paper introduces new variational formulation for reconstruction from subsampled dynamic cont... more This paper introduces new variational formulation for reconstruction from subsampled dynamic contrast-enhanced DCE-MRI data, that combines a data-driven approach using estimated temporal basis and total variation regularization (PCA TV). We also experimentally compares the performance of such model with two other state-of-the-art formulations. One models the shape of perfusion curves in time as a sum of a curve belonging to a low-dimensional space and a function sparse in a suitable domain (L + S model). The other possibility is to regularize both spatial and time domains (ICTGV). We are dealing with the specific situation of the DCE-MRI acquisition with a 9.4T small animal scanner, working with noisier signals than human scanners and with a smaller number of coil elements that can be used for parallel acquisition and small voxels. Evaluation of the selected methods is done through subsampled reconstruction of radially-sampled DCE-MRI data. Our analysis shows that compressed sensed MRI in the form of regularization can be used to increase the temporal resolution of acquisition while keeping a sufficient signal-to-noise ratio.

This paper is focused on quantitative perfusion analysis using pulsed ASL (FAIR-RARE) and DCE-MRI... more This paper is focused on quantitative perfusion analysis using pulsed ASL (FAIR-RARE) and DCE-MRI (using high-and low-molecular-weight contrast agents) in a mouse tumour model. Tumour blood-flow maps of both methods were compared using visual assessment, region analysis (median, percentiles), scatter plots and correlation coefficients. ASL blood-flow estimates matched the DCE-MRI blood-flow estimations in some cases. Possible reasons for poor match in the other cases were investigated. This study indicates that in tumour perfusion analysis, we might profit from the combination of ASL and DCE-MRI instead of using just one of them.

Magma, 2016

In vivo T(1) mapping of rat myocardium can be challenging given to the high heart and respiratory... more In vivo T(1) mapping of rat myocardium can be challenging given to the high heart and respiratory rate and small size of the heart. We propose a new method for T1 estimation based on retrospectively gated inversion-recovery fast low-angle shot (IR FLASH) pulse sequence. The method was applied and validated in a doxorubicin study.

In vivo diffusion tensor imaging (DTI) of rat thoracic spinal cord was performed on five healthy ... more In vivo diffusion tensor imaging (DTI) of rat thoracic spinal cord was performed on five healthy rats. Axial diffusion images were obtained using a standard spin echo diffusion weighted sequence. The fractional anisotropy (FA), longitudinal (LD) and transverse (TD) diffusivities and the mean diffusivity were estimated. Differences in these parameters between white and grey matter were in accord with theory and in the range reported in literature.

The aim of this study was to investigate Mag 102-6, a maghemite hybrid drug nanocarrier, as a pot... more The aim of this study was to investigate Mag 102-6, a maghemite hybrid drug nanocarrier, as a potential T 2 contrast agent (CA) for magnetic resonance imaging (MRI). Samples of agar gel mixed with different Fe concentrations of Mag 102-6 were measured at laboratory temperature for relaxivity r 2 determination in 9.4 T. The results were compared with commercial CA FeraSpin XXL measured in the same arrangement. In addition, the r 2 of Mag 102-6 in saline solution at physiological temperature 37.7°C was measured. MRI was performed with four mice using a 9.4T NMR scanner before, and up to 24 h post-injection (p.i.) of Mag 102-6 (dose 5 mg Fe kg-1). Images of abdomen were continuously acquired by segmented Multi Gradient Echo (MGE) pulse sequence from 1 minute before the CA application to 20 minutes p.i. The T 1-weighted (T 1-w) and T 2-weighted (T 2-w) images were captured before the application and 25 minutes, 3.5, 7 and 24 hours after CA application. R 2 * changes in time were estimated from MGE images for various anatomical regions (kidney, muscles, liver) by fitting of signal intensities. Mag 102-6 and FeraSpin XXL had comparable r 2 values. Mag 102-6 showed the potential to be monitored by MRI as a T 2 CA.

IFMBE proceedings, May 30, 2018

Dynamic contrast-enhanced magnetic resonance imaging obtains information about tissue perfusion a... more Dynamic contrast-enhanced magnetic resonance imaging obtains information about tissue perfusion and permeability. Following the administration of a contrast agent, concentration-time curves measured in each voxel are fitted by a pharmacokinetic model formulated as a time-domain convolution of an arterial input function (AIF) and an impulse residue function (IRF). Since the measurement window contains hundreds of time samples, the discrete convolution is demanding, even when it is performed via discrete Fourier transform (DFT). Additionally, its discretization causes convergence complications in the curve fitting and it is not applicable to functions without a closed-form expression in the time domain, e.g. tissue homogeneity model IRF. Both issues can be solved by formulating the functions in a closed form in the Fourier domain. In the Fourier domain, the model transforms to multiplication of IRF and AIF, followed by the inverse DFT. To avoid time-domain aliasing, the number of samples in the Fourier domain must be higher than the sum of supports of the functions in the time domain. If the functions are slowly decaying exponentials, the support is theoretically infinite, which dramatically reduces the computational performance. In this contribution, we propose a modification of IRF in the Fourier domain to consider the measurement window. Our solution reduces the required number of samples to three times the measurement window compared to dozens needed without the modification and reduces the number of DFTs. This provides faster evaluation of the pharmacokinetic model and its derivatives for each voxel in each iteration of the curve fitting.