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arXiv2017

Bio-inspired surface coil for small-bore MRI at 15.2 T

We looked for a biological analogy to developed an improved surface coil to acquire magnetic resonance images. Nature offers engineering solutions that can be exploited to improve the performance of devices, such as MRI RF coils. In this paper, we proposed a coil layout based on flower petal patterns for UHF MRI at 15.2 T. This particular configuration offers the possibility to use a different number of petals and shapes. The petal resonator coil and the magnetron coil have similar layouts, which have proved to outperform the popular circular coil. Phantom images were acquired with our coil prototype to demonstrate it feasibility. These phantom images show no image degradation caused by the mutual inductance of the adjacent petals in both orientations. The SNR was also calculated using the image data and giving 31.16. Phantom images showed the coil viability and compatibility with conventional pulse sequences at 15.2 T. It still remains to investigate whether this bio-inspired surface coil is able to outperformed the popular circular coil.

physics.med-ph↗

arXiv2017

A new radiobiology-based HDR brachytherapy treatment planning algorithm used to investigate the potential for hypofractionation in cervical cancer

Most commercially available treatment planning systems for brachytherapy operate based on physical dose and do not incorporate fractionation or tissue-specific response. The purpose of this study is to investigate the potential for hypofractionation in HDR brachytherapy, thereby reducing the number of implants required. A new treatment planning algorithm was built in order to optimize based on tissue and fractionation specific parameters. Different fractionation schemes were considered for 6 patients, and plans were created using the new algorithm. A baseline fractionation scheme consisting of 5 fractions was compared to hypofractionated plans of 1 to 4 fractions. The effectiveness of each plan was evaluated using radiobiological criteria taken from GEC-ESTRO guidelines. The results of this study indicate that an optimization algorithm based on biological parameters has similar functionality to traditional planning methods with the additional ability to account for fractionation effects. Using this algorithm, it was shown that plans consisting of 3 and 4 fractions have comparable target coverage with equivalent normal tissue exposure. In some specific cases, further fractionation may present acceptable target coverage as well.

physics.med-ph↗

arXiv2018

Investigation of the energy shielding of kidney stones by cavitation bubble clouds during burst wave lithotripsy

We conduct experiments and numerical simulations of the dynamics of bubble clouds nucleated on the surface of an epoxy cylindrical stone model during burst wave lithotripsy (BWL). In the experiment, the bubble clouds are visualized and bubble-scattered acoustics are measured. In the numerical simulation, we combine methods for modeling compressible multicomponent flows to capture complex interactions among cavitation bubbles, the stone, and the burst wave. Quantitative agreement is confirmed between results of the experiment and the simulation. We observe and quantify a significant shielding of incident wave energy by the bubble clouds. The magnitude of shielding reaches up to 80% of the total acoustic energy of the incoming burst wave, suggesting a potential loss of efficacy of stone comminution. We further discovered a strong linear correlation between the magnitude of the energy shielding and the amplitude of the bubble-scattered acoustics, independent of the initial size and the void fraction of the bubble cloud within a range addressed in the simulation. This correlation could provide for real-time monitoring of cavitation activity in BWL.

physics.med-ph↗

arXiv2018

Ex Vivo Mouse Brain Microscopy at 15T with Loop-Gap RF Coil

The design of a loop-gap-resonator RF coil optimized for ex vivo mouse brain microscopy at ultra high fields is described and its properties characterized using simulations, phantoms and experimental scans of mouse brains fixed in 10% formalin containing 4 mM Magnevist. The RF (B1) and magnetic field (B0) homogeneities are experimentally quantified and compared to electromagnetic simulations of the coil. The coil's performance is also compared to a similarly sized surface coil and found to yield double the sensitivity. A three-dimensional gradient-echo (GRE) sequence is used to acquire high resolution mouse brain scans at 47 μm3 resolution in 1.8 hours and a 20x20x19 μm3 resolution in 27 hours. The high resolution obtained permitted clear visualization and identification of multiple structures in the ex vivo mouse brain and represents, to our knowledge, the highest resolution ever achieved for a whole mouse brain. Importantly, the coil design is simple and easy to construct.

physics.med-ph↗

arXiv2019

An Improved Method of Total Variation Superiorization Applied to Reconstruction in Proton Computed Tomography

Previous work showed that total variation superiorization (TVS) improves reconstructed image quality in proton computed tomography (pCT). The structure of the TVS algorithm has evolved since then and this work investigated if this new algorithmic structure provides additional benefits to pCT image quality. Structural and parametric changes introduced to the original TVS algorithm included: (1) inclusion or exclusion of TV reduction requirement, (2) a variable number, $N$, of TV perturbation steps per feasibility-seeking iteration, and (3) introduction of a perturbation kernel $0<α<1$. The structural change of excluding the TV reduction requirement check tended to have a beneficial effect for $3\le N\le 6$ and allows full parallelization of the TVS algorithm. Repeated perturbations per feasibility-seeking iterations reduced total variation (TV) and material dependent standard deviations for $3\le N\le 6$. The perturbation kernel $α$, equivalent to $α=0.5$ in the original TVS algorithm, reduced TV and standard deviations as $α$ was increased beyond $α=0.5$, but negatively impacted reconstructed relative stopping power (RSP) values for $α>0.75$. The reductions in TV and standard deviations allowed feasibility-seeking with a larger relaxation parameter $λ$ than previously used, without the corresponding increases in standard deviations experienced with the original TVS algorithm. This work demonstrates that the modifications related to the evolution of the original TVS algorithm provide benefits in terms of both pCT image quality and computational efficiency for appropriately chosen parameter values.

physics.med-ph↗

arXiv2018

Generation of Infra sound to replicate a wind turbine

We have successfully produced infrasound, as a duplicate of that produced by Industrial Wind Turbines. We have been able to produce this Infrasound inside a research chamber, capable of accommodating a human test subject. It is our vision that this project will permit others, with appropriate medical training and ethical oversight, to research human thresholds and the effects of this infrasound on humans. Our role has focused on producing the tools, systems, and hardware required, to permit this research to go forward. This paper describes the evolution of our project from the original vision, through the construction of proof of concept prototypes, a series of improved models and their associated accessories /operating systems, to the final test chamber as it stands now ready to deploy. Also included are the mathematical and computational data supporting our claim that infrasound conditions inside the chamber can be made to duplicate those from actual Industrial wind turbines at approved setback distances.

cs.SD↗

arXiv2018

A generative model of realistic brain cells with application to numerical simulation of diffusion-weighted MR signal

In this work, we introduce a novel computational framework that we developed to use numerical simulations to investigate the complexity of brain tissue at a microscopic level with a detail never realised before. Directly inspired by the advances in computational neuroscience for modelling brain cells, we propose a generative model that enables us to simulate molecular diffusion within realistic digitalised brain cells, such as neurons and glia, in a completely controlled and flexible fashion. We validate our new approach by showing an excellent match between the morphology and simulated DW-MR signal of the generated digital model of brain cells and those of digital reconstruction of real brain cells from available open-access databases. We demonstrate the versatility and potentiality of the framework by showing a select set of examples of relevance for the DW-MR community. Further development is ongoing, which will support even more realistic conditions like dense packing of numerous 3D complex cell structures and varying cell surface permeability.

physics.med-ph↗

arXiv2018

Quantitative MRI: Absolute T1, T2 and Proton Density Parameters from Deep Learning

Quantitative MRI is highly desirable in terms of intrinsic tissue parameters such as T1, T2 and proton density. This approach promises to minimize diagnostic variability and differentiate normal and pathological tissues by comparing tissue parameters to the normal ranges. Also, absolute quantification can help segment MRI tissue images with better accuracy compared to traditional qualitative segmentation methods. Currently, there are several methods proposed to quantify tissue parameters; however, all of them require excessive scan time and thus are difficult to be applied in clinical applications. In this paper, we propose a novel machine learning approach for MRI quantification, which can dramatically decrease the scan time and improve image quality.

physics.med-ph↗

arXiv2018

A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology

The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei are known to have different functions and to be connected to different areas of the cerebral cortex, it is of great interest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manual delineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combined with manual segmentations of the whole thalamus and surrounding structures (caudate, putamen, hippocampus, etc.) made on in vivo brain MR data from 39 subjects. The 3D structure of the histological data and corresponding manual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographs acquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptive tetrahedral mesh, shows a good agreement with with previous histological studies of the thalamus in terms of volumes of representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas shows excellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differential thalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool are publicly available as part of the neuroimaging package FreeSurfer.

q-bio.NC↗

arXiv2018

Dynamics of Insufflated Abdominal Wall Tissue for Magnetically Anchored Surgical Instruments

Magnetically-anchored surgical devices have recently gained attention in abdominal surgery, with the use of magnets to anchor surgical devices onto the insufflated abdominal wall. These anchors have been used to secure passive and active devices, where active device such as robotic manipulators produce motions that would excite the dynamics of the non-rigid abdominal wall. Hence, there is a need to investigate the mechanical dynamics of the abdominal wall tissue in insufflated state, combined with magnetic anchoring, specifically its response to mechanical excitations and the expected disturbances to the operation of the anchored devices. In this paper, loading and unloading tests are performed on a corresponding porcine specimen for dynamics identification. The experiment setup was constructed to emulate the insufflated state of the abdomen with the magnetically anchored mechanism. The tissue responses during unloading are captured and approximated with a general numerical model, which is in turn used for the dynamic analysis of the tissue using Bode plot. The results showed that in such stretched and compressed state, the steady state displacement of the tissue is approximately zero. The maximum transient error was found to be 1mm in displacement using a high magnetic anchoring force. Significant attenuation of the disturbances due to the high stiffness and damping of the abdominal wall, was observed from 100rad/s in the frequency response. If a robotic manipulator was attached to the anchoring device, the typical operating frequency of movements would still produce unattenuated disturbances. It is expected that some error compensation through suitable control strategies is required. These outcomes establish the basis for the controller design and the design specification of the active magnetically-anchored surgical devices for minimal disturbance impact onto the abdominal wall tissue.

physics.med-ph↗

arXiv2018

Environmental Lead-210 gamma-ray measurements in brain tumors

In 2006 Momčilović et al. measured radioactvity levels of 210Po and 210Bi by alpha- and beta-measurements resp. to determine the natural distribuion of environmental radon daughters in the different brain areas of an Alzheimer Disease victim. We show that gamma-ray spectrometry of the mother nucleus 210Pb can be used. It is a direct measurement without tampering with the sample. However, because this technique is far less sensitive than alpha- and beta-spectrometry, activity values previously published were out-of-reach for gamma-ray spectrometry. This is no longer the case with our ultra-low background high purity Ge detectors which have been developed in the frame of the neutrino experiments. To ascertain this possibility, ten brain samples from Alzheimer patients and blanks as well as 10 samples of brain tumors have been investigated and results were cross-checked with two different spectrometers. Localization of the samples in the brain was not known to avoid biased interpretation of the results. Data taking lasted between 1 and 4 weeks for each sample. All ten Alzheimer/blank samples were below the limit of detection (LOD), 3 out of the 10 tumors lead to positive results (3.8 to 4.9 mBq/g of 210Pb) with a statistical significance of at least 3 standard deviations. Potential followup of this method is to enhance the detector sensitivity, having the spectrometer installed in an underground laboratory such as the one in Modane under the Alps where the background noise is 30- fold less than at the present location in Bordeaux. The final aim is to map a brain in collaboration with Alzheimer/Parkinson experts.

physics.med-ph↗

arXiv2018

Segmentation of TCD Cerebral Blood Flow Velocity Recordings

A binary beat-by-beat classification algorithm for cerebral blood flow velocity (CBFV) recordings based on amplitude, spectral and morphological features is presented. The classification difference between 15 manually and algorithmically annotated CBFV records is around 5%.

eess.SP↗

arXiv2018

Influence of patient alignment on image quality provided by a C-arm flat-panel detector computer tomography: a phantom study

Purpose: The aim of this phantom study was to evaluate the influence of patient alignment on the image quality by a C-arm flat-panel detector computer tomography (CACT). Materials and Methods: An ACR phantom placed in two opposite directions along the z-Axis was imaged using a CACT. Image acquisition was performed by three different image acquisition protocols using fixed X-ray tube voltages of 81, 102 and 125 kVp. The images were reconstructed with four different convolution kernels, i.e. normal, sharp, soft and very soft. Image quality was assessed in terms of high contrast image quality using the modulation transfer function (MTF) and low contrast image quality by assessing the signal-to-noise ratio (SNR) and contrast-to-noise ratios (CNR) as well as reliability of density measurements. Furthermore, the dose intensity profiles parallel and perpendicular to the patient support were measured free-in-air. Results: The intensity profile of the CACT measured by the detector system free-in-air showed that the anode heel effect is not in the longitudinal direction to the z-axis. The image noises measured in Setup A for the air and bone inserts were systematically higher compared to those measured in Setup B, in average about 3% and 4% for the air and bone inserts, respectively. An opposite behavior has been observed for the polyethylene, water-equivalent and acrylic inserts. The corresponding image noises were in average about 4%, 6% and 2% lower measured in Setup A compared to those measured in Setup B. SNR for all inserts behaves inversely to the image noise. Conclusion: The patient alignment has a minor influence on the image quality of CACT. This effect is not based on the X-ray anode heel effect. It is caused mainly. This effect is caused mainly by the non-symmetrical rotation of the CACT.

physics.med-ph↗

arXiv2018

An Exploration of Spatial Radiomic Features in Pulmonary Sarcoidosis

Sarcoidosis is a rare, multi-systemic, inflammatory disease, primarily affecting the lungs. High-resolution computed tomography (CT) scans are used to clinically characterize pulmonary sarcoidosis. In the medical imaging field, there is growing recognition to switch from visual examination of CT images to more rapid, objective assessments of the abnormalities. In this work, we explore the usefulness of various objective measures of spatial heterogeneity---fractal dimension, Moran's I, and Geary's C ---for distinguishing between abnormal sarcoidosis and normal lung parenchyma. CT data for N=58 sarcoidosis subjects enrolled at National Jewish Health were obtained from the GRADS study. CT data for N=101 control patients were obtained from the COPDGene study. Radiomic measures were computed for each two-dimensional slice of a given scan, in the axial, coronal, and sagittal planes. Functional regression was applied to identify lung regions where CT nodules tend to proliferate. Moran's I, Geary's C and fractal dimension significantly differentiate between subjects with and without sarcoidosis throughout the majority of the lung, with disease abnormalities most apparent in the top axial, middle coronal, and outer sagittal regions. A trend appeared across Scadding stages, with CT scans from patients with Scadding stages I and III appearing the healthiest, and Scadding stage IV appearing the least healthy. The radiomic measures and techniques presented herein successfully characterize CT images in sarcoidosis by objectively and efficiently approximating what we know about the pathology of sarcoidosis.

physics.med-ph↗

arXiv2018

Fe3O4@astragalus polysaccharide core-shell nanoparticles for iron deficiency anemia therapy and magnetic resonance imaging in vivo

Fe3O4@astragalus polysaccharide core-shell nanoparticles (Fe3O4@APS NPs) were demonstrated to be an efficient therapeutic drug for treating iron deficiency anemia (IDA) in vivo. The Fe3O4@APS NPs have been synthesized using a two steps approach involving hydrothermal synthesis and subsequent esterification. Transmission electron microscopy (TEM) and Fourier transform infrared (FTIR) spectroscopy studies show that APS are attached on the surfaces of the highly monodisperse Fe3O4 NPs. Dynamic light scatting (DLS) and magnetic characterizations reveal that the Fe3O4@APS NPs have outstanding water solubility and stability. Cytotoxicity assessment using Hela cells and pathological tests in mice demonstrate their good biocompatibility and low toxicity. The IDA treatment in rats shows that they have efficient therapeutic effect, which is contributed to both the iron element supplement from Fe3O4 and the APS-stimulated hematopoietic cell generation. Moreover, the Fe3O4@APS NPs are superparamagnetic and thus able to be used for magnetic resonance imaging (MRI). This study has demonstrated the potential of nanocomposites involving purified natural products from Chinese herb medicine for biomedical applications.

physics.bio-ph↗

arXiv2018

High Sensitivity Collimators for Optimising Lesion Detection in SPECT Images

Parallel hole collimators which are currently routinely used in SPECT imaging were designed a few decades ago, when filtered backprojection (FBP) was used for tomographic reconstruction. Statistical reconstruction methods with precise modeling of the projection measurement offer a different standard, and the question of optimizing resolution - sensitivity tradeoff by choosing appropriate collimator aperture needs to be revised. In this paper we search for a parallel hole collimator which offers best performance in detection of hot lesions on a uniform background. To evaluate the image quality we use standard quantitative measures like the contrast recovery coefficient, coefficient of variation, and contrast to noise ratio. We also performed signal detection by human observers followed by Receiver Operating Characteristics (ROC) analysis for a few lesions close to the limit of visibility. Our results consistently indicate that optimal performance is achieved with collimators of sensitivity 6 - 9 times that of the conventional high resolution (HR) collimator. When the optimized collimator is applied, the image quality of the conventional image obtained with the HR can be achieved at scanning time or activity dose reduced by factor of 3.

physics.med-ph↗

arXiv2018

Reduced effective scanning time in SPECT due to OSEM accelerated reconstruction

We study the increase of image noise which can be observed in images reconstructed with the OSEM algorithm. We argue that the excessive noise is equivalent to shortening scanning time by a factor of 2 or more at high number of subsets (acceleration factors). Therefore, by keeping the number of OSEM subsets low one can significantly reduce image noise, which in turn is equivalent to increasing scanning time or radiation dose. While the OSEM remains a very useful reconstruction method enabling substantial reduction of reconstruction times, it should be used with caution. In particular, high numbers of subsets should be avoided if possible. Whenever the available computing power allows achieving acceptable reconstruction times at lower number of subsets, one can consider reducing scanning time or injected dose, while maintaining the image quality of standard scans reconstructed with higher OSEM acceleration. The recommended maximal "safe" number of subsets, which does not lead to significant increase of image noise, is about 5.

physics.med-ph↗

arXiv2018

An EDUGATE simulation toolkit based on the educational easyPET

EasyPET is a new concept of a Positron Emission Tomography (PET) scanner using an innovative acquisition method based on two rotation axes for the movement of detector pairs. Due to its simplicity, it is suitable for education purposes, to teach students about the PET technology and its basic concepts, from the radiation detecting and analogue pulse analysis to the coincidence sorting and image reconstruction. The concept allows achieving high and uniform position resolution over the whole field of view (FoV), by eliminating parallax errors due to the depth of interaction (DoI), which are typical of ring-based PET systems, so quality images are obtained even without state-of-the-art image reconstruction algorithms. The technology developed at the University of Aveiro with a patent-pending, is licensed to CAEN S.p.A, and included in the educational catalogue of the company. In this work, a simulation toolkit based in the Edugate platform was developed to simulate the EasyPET system. It can simulate all the physical aspects of the product, such us the scanning range, variable Field-of-View (FOV), scintillator energy resolution, coincidence time and energy window, among others. A simple image reconstruction algorithm based on Filtered-back-projection (FBP) is implemented. The toolkit allows a quick analysis in classroom of the simulation results. The platform was also used to study the new EasyPET 3D version, and a simulation of a NEMA NU 4-2008 IQ phantom was performed, demonstrating the capability of the platform not only for education purposes but also for research. Patent Universidade de Aveiro: PCT/IB2016/051487

physics.med-ph↗