Matthew Orton - Academia.edu (original) (raw)

Papers by Matthew Orton

Journal of magnetic resonance imaging : JMRI, Jan 8, 2016

To assess the correlation between each of intravoxel incoherent motion diffusion-weighted imaging... more To assess the correlation between each of intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) metrics in renal parenchyma with renal function, in a cohort of patients with chronic liver disease. Thirty patients with liver disease underwent abdominal MRI at 1.5T, including a coronal respiratory-triggered IVIM-DWI sequence and a coronal 3D FLASH DCE-MRI acquisition. Diffusion signals in the renal cortex and medulla were fitted to the IVIM model to estimate the diffusion coefficient (D), pseudodiffusion coefficient (D*), and perfusion fraction (PF). The apparent diffusion coefficient (ADC) was calculated using all b-values. The glomerular filtration rate (GFR), cortical and medullary renal plasma flow (RPF), mean transit times (MTT) of vascular and tubular compartments and the whole kidney, were calculated from DCE-MRI data by fitting to a three-compartment model. The estimated GFR (eGFR) was calculated f...

Journal of magnetic resonance imaging : JMRI, Jan 19, 2016

The significant advances in magnetic resonance imaging (MRI) hardware and software, sequence desi... more The significant advances in magnetic resonance imaging (MRI) hardware and software, sequence design, and postprocessing methods have made diffusion-weighted imaging (DWI) an important part of body MRI protocols and have fueled extensive research on quantitative diffusion outside the brain, particularly in the oncologic setting. In this review, we summarize the most up-to-date information on DWI acquisition and clinical applications outside the brain, as discussed in an ISMRM-sponsored symposium held in April 2015. We first introduce recent advances in acquisition, processing, and quality control; then review scientific evidence in major organ systems; and finally describe future directions. J. Magn. Reson. Imaging 2016.

Images are very highly dimensional datasets. The use of statistical inference in the processing o... more Images are very highly dimensional datasets. The use of statistical inference in the processing of images necessitates the use of algorithms that scale linearly with the number of pixels. In Lavine&amp;amp;amp;#39;s paper, &amp;amp;amp;amp;amp;quot;Another Look at Conditionally Gaussian Markov Random Fields&amp;amp;amp;amp;amp;quot; and Rue&amp;amp;amp;#39;s paper &amp;amp;amp;amp;amp;quot;Fast Sampling of Gaussian Makov Random Fields with Applications&amp;amp;amp;amp;amp;quot; methods are proposed that scale quadratically with the

Physics in Medicine and Biology, Mar 7, 2008

A description of the vascular input function is needed to obtain tissue kinetic parameter estimat... more A description of the vascular input function is needed to obtain tissue kinetic parameter estimates from dynamic contrast enhanced MRI (DCE-MRI) data. This paper describes a general modelling framework for defining compact functional forms to describe vascular input functions. By appropriately specifying the components of this model it is possible to generate models that are realistic, and that ensure that the tissue concentration curves can be analytically calculated. This means that the computations necessary to estimate parameters from measured data are relatively efficient, which is important if such methods are to become of use in clinical practice. Three models defined by four parameters, using exponential, gamma-variate and cosine descriptions of the bolus, are described and their properties investigated using simulations. The results indicate that if there is no plasma fraction, then the proposed models are indistinguishable. When a small plasma fraction is present the exponential model gives parameter estimates that are biassed by up to 50%, while the other two models give very little bias; up to 10% but less than 5% in most cases. With a larger plasma fraction the exponential model is again biassed, the gamma-variate model has a small bias, but the cosine model has a very little bias and is indistinguishable from the model used to generate the data. The computational speed of the analytic approaches is compared with a fast-Fourier-transform-based numerical convolution approach. The analytic methods are nearly 10 times faster than the numerical methods for the isolated computation of the convolution, and around 4-5 times faster when used in an optimization routine to obtain parameter estimates. These results were obtained from five example data sets, one of which was examined in more detail to compare the estimates obtained using the different models, and with literature values.

ABSTRACT When fusing the information from several sensors the possibility that measurements are r... more ABSTRACT When fusing the information from several sensors the possibility that measurements are received in the wrong order must be considered. This is especially true if the sensors are of dierent types, or if human observations are to be included. Recent advances in the eld of Monte Carlo sampling procedures, particularly the Particle Filter, allow for the sequential tracking of non-linear and non-gaussian dynamic systems using a cloud of samples. We build on this to generate an algorithm capable of incorporating out-of-sequence measurements (OOSMs) in the general non-linear non-gaussian framework.

Journal of magnetic resonance imaging : JMRI, Jan 20, 2015

To investigate the clinical utility of the reverse gradient algorithm in correcting distortions i... more To investigate the clinical utility of the reverse gradient algorithm in correcting distortions in diffusion-weighted images of the cervix and for increasing diagnostic performance. Forty-one patients ages 25-72 years (mean 40 ± 11 years) with suspected or early stage cervical cancer were imaged at 3T using an endovaginal coil. T2 -weighted (W) and diffusion-weighted images with right and left phase-encode gradient directions were obtained coronal to the cervix (b = 0, 100, 300, 500, 800 s mm(-2) ). Differences in angle of the endocervical canal to the x-axis between T2 W and right-gradient, left-gradient, and corrected images were measured. Uncorrected and corrected images were assessed for diagnostic performance when viewed together with T2 W images by two independent observers against subsequent histology. The angles of the endocervical canal relative to the x-axis were significantly different between the T2 W images and the right-gradient images (P = 0.007), approached significa...

European radiology, Jan 18, 2015

Pharmacokinetic (PK) modelling of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) ... more Pharmacokinetic (PK) modelling of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data requires a reliable measure of the arterial input function (AIF) to robustly characterise tumour vascular properties. This study compared repeatability and treatment-response effects of DCE-MRI-derived PK parameters using a population-averaged AIF and three patient-specific AIFs derived from pre-bolus MRI, DCE-MRI and dynamic contrast computed tomography (DC-CT) data. The four approaches were compared in 13 patients with abdominal metastases. Baseline repeatability [Bland-Altman statistics; coefficient of variation (CoV)], cohort percentage change and p value (paired t test) and number of patients with significant DCE-MRI parameter change post-treatment (limits of agreement) were assessed. Individual AIFs were obtained for all 13 patients with pre-bolus MRI and DC-CT-derived AIFs, but only 10/13 patients had AIFs measurable from DCE-MRI data. The best CoV (7.5 %) of the transfer coe...

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Bone metastases in men with advanced prostate cancer were examined by diffusion MRI with varying ... more Bone metastases in men with advanced prostate cancer were examined by diffusion MRI with varying diffusion times and gradient strengths. Data were fitted to 3-compartment models of diffusion that included a perfusion compartment, an extracellular compartment and an intracellular spherically-restricted compartment. Data showed variation for points with the same b-value but different diffusion time and were better explained by a model incorporating restriction than either conventional ADC or 2- or 3-compartment models with free diffusion. Model parameters indicated a low perfusion fraction (<10%), intracellular volume fraction 0.22-0.56 and a cell radius between 4.7-9.9 µm.

Diffusion-weighted MRI in the body must account for a microcirculation fraction, separate to self... more Diffusion-weighted MRI in the body must account for a microcirculation fraction, separate to self-diffusion, within imaging voxels. Explicit control of diffusion pulse length and delay allows reproducible application of diffusion gradients with varying echo times; calculation of mono-exponential T2 estimates with applied gradients of b=0 and b=200 s/mm2 shows significant changes observed in liver, kidney and spleen. This suggests that the microcirculation component, with its own distinct T2, is being removed, allowing the generation of flow-free T2 maps more robustly estimating tissue T2s. This approach enables appropriate b-value choices when considering diffusion models that include or exclude microcirculation contribution.

The intra-voxel incoherent motion (IVIM) model relates signal decay on diffusion-weighted MRI (DW... more The intra-voxel incoherent motion (IVIM) model relates signal decay on diffusion-weighted MRI (DWI) to tissue characteristics of perfusion and diffusivity. We explored the effects of altering the diffusion time of DWI sequences on IVIM perfusion (f,D*) and diffusion (D) related parameters in abdominal organs of healthy volunteers. At longer diffusion times, the calculated perfusion fraction (f) was significantly increased while the effect on the D and D* parameters was more variable, depending on the organ under study. The diffusion time has a significant impact on measured IVIM parameters in abdominal organs and should be reported when employing the IVIM model.

Respiratory motion commonly confounds abdominal DWI, and motion minimisation strategies adversely... more Respiratory motion commonly confounds abdominal DWI, and motion minimisation strategies adversely affect scan efficiency and comfort. Blurring is due to post-acquisition combination of images from separate signal averages and diffusion-gradient directions, and is not inherent to the images. In a volunteer cohort where all images were stored separately, taking a (voxel-by-voxel) median image instead of a mean at each b-value yields parameter maps with much improved sharpness while still retaining tissue features. ADCs from ROIs in liver and kidneys were 108±18 vs 120±26 (p=0.007) and 182±17 vs 188±13 (p=0.04) x10-5 mm2s-1 for median and mean, respectively.

2011 10th International Conference on Machine Learning and Applications and Workshops, 2011

ABSTRACT The topic of deep-learning has recently received considerable attention in the machine l... more ABSTRACT The topic of deep-learning has recently received considerable attention in the machine learning research community, having great potential to liberate computer scientists from hand-engineering training datasets, because the method can learn the desired features automatically. This is particularly beneficial in medical research applications of machine learning, where getting good hand labelling of data is especially expensive. We propose application of a single-layer sparse-auto encoder to dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) for fully automatic classification of tissue types in a large unlabelled dataset with minimal human interference -- in a manner similar to data-mining. DCE-MRI analysis, looking at the change of the MR contrast-agent concentration over successively acquired images, is time-series analysis. We analyse the change of brightness (which is related to the contrast-agent concentration) of the DCE-MRI images over time to classify different tissue types in the images. Therefore our system is an application of an auto encoder to time-series analysis while the demonstrated result and further possible successive application areas are in computer vision. We discuss the important factors affecting performance of the system in applying the auto encoder to the time-series analysis of DCE-MRI medical image data.

Physics in medicine and biology, Jan 21, 2015

Respiratory motion commonly confounds abdominal diffusion-weighted magnetic resonance imaging, wh... more Respiratory motion commonly confounds abdominal diffusion-weighted magnetic resonance imaging, where averaging of successive samples at different parts of the respiratory cycle, performed in the scanner, manifests the motion as blurring of tissue boundaries and structural features and can introduce bias into calculated diffusion metrics. Storing multiple averages separately allows processing using metrics other than the mean; in this prospective volunteer study, median and trimmed mean values of signal intensity for each voxel over repeated averages and diffusion-weighting directions are shown to give images with sharper tissue boundaries and structural features for moving tissues, while not compromising non-moving structures. Expert visual scoring of derived diffusion maps is significantly higher for the median than for the mean, with modest improvement from the trimmed mean. Diffusion metrics derived from mono- and bi-exponential diffusion models are comparable for non-moving stru...

ABSTRACT Purpose: To assess the feasibility of accurately quantifying the concentration of MRI co... more ABSTRACT Purpose: To assess the feasibility of accurately quantifying the concentration of MRI contrast agent (CA) in pulsatile flowing blood by measuring its T1, as is common for the purposes of obtaining a patientspecific arterial input function (AIF). Dynamic contrast enhanced (DCE) - MRI and pharmacokinetic (PK) modelling is widely used to produce measures of vascular function but accurate measurement of the AIF undermines their accuracy. A proposed solution is to measure the T1 of blood in a large vessel using the Fram double flip angle method during the passage of a bolus of CA. This work expands on previous work by assessing pulsatile flow and the changes in T1 seen with a CA bolus.