Methods for evaluating geometric distortion in magnetic resonance imaging

Abstract. Geometric distortions and spatial inaccuracies in magnetic resonance imaging are an important concern especially in image-guided high accuracy operations, such as radiotherapy or stereotactic surgeries. Geometric distortions in the images are in principle caused by erroneous spatial encoding of the signal echo. Errors in the spatial encoding are caused by different physical factors, such as static field inhomogeneity, gradient field nonlinearities, chemical shift, and magnetic susceptibility. The distortion shifts can be quantitatively evaluated as the amount of distance or pixels that a signal source has shifted in the mapping from real space to the image space. By studying the distortions and the causing mechanisms, corrective measures can be taken to minimize spatial errors in the images. In this thesis the geometric distortions of one MRI scanner are evaluated with four different grid phantom objects. The scanner was a 3 Tesla scanner at the Oulu University Hospital. The phantoms included two commercial readily available MRI quality assurance phantoms and two in-house produced prototype phantoms. The methods consisted of imaging the phantoms with different two- and three- dimensional sequences. Image and distortion analysis was performed with one commercial distortion check software for the respective commercial phantom, and with an in-house developed Matlab program for all four phantoms. Results for the magnitude and direction of the distortion as a function of distance from the scanner isocenter were acquired. Three-dimensional distortion shifts up 4 mm within a radius of 200 mm from the isocenter were measured, with occasional shifts up to 9 mm between 100 and 200 mm from the isocenter. Distortion field maps and contour plots produced with both analysis methods seemed to be in accordance with each other, and the geometry and behaviour of the field was found to be as expected. As to the prototype phantoms, a result with respect to the grid density was found. A 5 mm grid separation was too dense with respect to the achievable resolution for the Matlab analysis script to function, or more generally for any distortion check at all.Tiivistelmä. Magneettikuvien geometriset vääristymät ja epätarkkuudet ovat tärkeitä huomioon otettavia asioita erityisesti sädehoitoihin tai kirurgisiin operaatioihin liittyvissä kuvantamisissa. Kuvien vääristymät aiheutuvat virheistä signaalien paikkakoodauksessa. Paikkakoodaukseen aiheutuu virheitä eri fysikaalisista tekijöistä, kuten staattisen magneettikentän epähomogeenisuuksista, gradienttikenttien epälineaarisuuksista, kemiallisesta siirtymästä tai magneettisesta suskeptibiliteetistä. Geometrinen vääristymä voidaan määrittää kvantitatiivisesti tutkimalla signaalin paikan siirtymää kuvauksessa todellisesta koordinaatistosta, eli kuvattavasta kohteesta, kuvan koordinaatistoon. Kuvia voidaan myös korjata vääristymien osalta tutkimalla vääristymien luonnetta ja niiden aiheuttajia. Tässä tutkielmassa tutkittiin Oulun yliopistollisen sairaalan yhden 3 Teslan kenttävoimakkuuden magneettikuvauslaitteen geometrista vääristymää. Kuvauksissa käytettiin neljää erilaista fantomia, kahta valmista kaupallisesti saatavilla olevaa sekä kahta kokeellista prototyyppiä. Fantomeita kuvattiin eri kaksi- ja kolmiulotteisilla kuvaussekvensseillä. Kuva- ja vääristymäanalyysiä varten käytettiin yhtä kaupallista ohjelmaa, joka on tarkoitettu sitä vastaavalle fantomille, sekä itse sairaalassa kehitettyä Matlab-pohjaista ohjelmaa. Mittausten perusteella saatiin kvantitatiiviset tulokset vääristymän suuruudelle ja suunnalle, etäisyyden funktiona skannerin keskipisteestä. Kolmiulotteisten vääristymien suuruudet olivat 4 mm tai alle 200 mm säteelle asti, suurimpien yksittäisten vääristymien ollessa noin 9 mm tai alle 100 mm ja 200 mm etäisyyksien välillä. Molemmilla analyysiohjelmilla vääristymien suuntien perusteella luodut vektorikentät olivat toistensa mukaisia ja vääristymän käyttäytyminen vaikutti odotetulta. Prototyyppifantomien suhteen päädyttiin tulokseen, jonka mukaan 5 mm ruudukko oli liian tiheä suhteessa resoluutioon, eikä Matlab-pohjainen analyysi toiminut. Tarpeeksi leveä ruudukko oli siten oleellinen osa vääristymän määrittämistä

Tissue mimicking materials for imaging and therapy phantoms: a review

Tissue mimicking materials (TMMs), typically contained within phantoms, have been used for many decades in both imaging and therapeutic applications. This review investigates the specifications that are typically being used in development of the latest TMMs. The imaging modalities that have been investigated focus around CT, mammography, SPECT, PET, MRI and ultrasound. Therapeutic applications discussed within the review include radiotherapy, thermal therapy and surgical applications. A number of modalities were not reviewed including optical spectroscopy, optical imaging and planar x-rays. The emergence of image guided interventions and multimodality imaging have placed an increasing demand on the number of specifications on the latest TMMs. Material specification standards are available in some imaging areas such as ultrasound. It is recommended that this should be replicated for other imaging and therapeutic modalities. Materials used within phantoms have been reviewed for a series of imaging and therapeutic applications with the potential to become a testbed for cross-fertilization of materials across modalities. Deformation, texture, multimodality imaging and perfusion are common themes that are currently under development

Development of a temperature-controlled phantom for magnetic resonance quality assurance of diffusion, dynamic, and relaxometry measurements.

Purpose Diffusion-weighted (DW) and dynamic contrast-enhanced magnetic resonance imaging (MRI) are increasingly applied for the assessment of functional tissue biomarkers for diagnosis, lesion characterization, or for monitoring of treatment response. However, these techniques are vulnerable to the influence of various factors, so there is a necessity for a standardized MR quality assurance procedure utilizing a phantom to facilitate the reliable estimation of repeatability of these quantitative biomarkers arising from technical factors (e.g., B1 variation) affecting acquisition on scanners of different vendors and field strengths. The purpose of this study is to present a novel phantom designed for use in quality assurance for multicenter trials, and the associated repeatability measurements of functional and quantitative imaging protocols across different MR vendors and field strengths.Methods A cylindrical acrylic phantom was manufactured containing 7 vials of polyvinylpyrrolidone (PVP) solutions of different concentrations, ranging from 0% (distilled water) to 25% w/w, to create a range of different MR contrast parameters. Temperature control was achieved by equilibration with ice-water. Repeated MR imaging measurements of the phantom were performed on four clinical scanners (two at 1.5 T, two at 3.0 T; two vendors) using the same scanning protocol to assess the long-term and short-term repeatability. The scanning protocol consisted of DW measurements, inversion recovery (IR) T1 measurements, multiecho T2 measurement, and dynamic T1-weighted sequence allowing multiple variable flip angle (VFA) estimation of T1 values over time. For each measurement, the corresponding calculated parameter maps were produced. On each calculated map, regions of interest (ROIs) were drawn within each vial and the median value of these voxels was assessed. For the dynamic data, the autocorrelation function and their variance were calculated; for the assessment of the repeatability, the coefficients of variation (CoV) were calculated.Results For both field strengths across the available vendors, the apparent diffusion coefficient (ADC) at 0 °C ranged from (1.12 ± 0.01) × 10(-3) mm(2)/s for pure water to (0.48 ± 0.02) × 10(-3) mm(2)/s for the 25% w/w PVP concentration, presenting a minor variability between the vendors and the field strengths. T2 and IR-T1 relaxation time results demonstrated variability between the field strengths and the vendors across the different acquisitions. Moreover, the T1 values derived from the VFA method exhibited a large variation compared with the IR-T1 values across all the scanners for all repeated measurements, although the calculation of the standard deviation of the VFA-T1 estimate across each ROI and the autocorrelation showed a stability of the signal for three scanners, with autocorrelation of the signal over the dynamic series revealing a periodic variation in one scanner. Finally, the ADC, the T2, and the IR-T1 values exhibited an excellent repeatability across the scanners, whereas for the dynamic data, the CoVs were higher.Conclusions The combination of a novel PVP phantom, with multiple compartments to give a physiologically relevant range of ADC and T1 values, together with ice-water as a temperature-controlled medium, allows reliable quality assurance measurements that can be used to measure agreement between MRI scanners, critical in multicenter functional and quantitative imaging studies

MRI compatible miniature motor system: Proof of Concept

Master's Thesis in PhysicsPHYS399MAMN-PHY

PET/MR imaging of hypoxic atherosclerotic plaque using 64Cu-ATSM

ABSTRACT OF THE DISSERTATION PET/MR Imaging of Hypoxic Atherosclerotic Plaque Using 64Cu-ATSM by Xingyu Nie Doctor of Philosophy in Biomedical Engineering Washington University in St. Louis, 2017 Professor Pamela K. Woodard, Chair Professor Suzanne Lapi, Co-Chair It is important to accurately identify the factors involved in the progression of atherosclerosis because advanced atherosclerotic lesions are prone to rupture, leading to disability or death. Hypoxic areas have been known to be present in human atherosclerotic lesions, and lesion progression is associated with the formation of lipid-loaded macrophages and increased local inflammation which are potential major factors in the formation of vulnerable plaque. This dissertation work represents a comprehensive investigation of non-invasive identification of hypoxic atherosclerotic plaque in animal models and human subjects using the PET hypoxia imaging agent 64Cu-ATSM. We first demonstrated the feasibility of 64Cu-ATSM for the identification of hypoxic atherosclerotic plaque and evaluated the relative effects of diet and genetics on hypoxia progression in atherosclerotic plaque in a genetically-altered mouse model. We then fully validated the feasibility of using 64Cu-ATSM to image the extent of hypoxia in a rabbit model with atherosclerotic-like plaque using a simultaneous PET-MR system. We also proceeded with a pilot clinical trial to determine whether 64Cu-ATSM MR/PET scanning is capable of detecting hypoxic carotid atherosclerosis in human subjects. In order to improve the 64Cu-ATSM PET image quality, we investigated the Siemens HD (high-definition) PET software and 4 partial volume correction methods to correct for partial volume effects. In addition, we incorporated the attenuation effect of the carotid surface coil into the MR attenuation correction _-map to correct for photon attention. In the long term, this imaging strategy has the potential to help identify patients at risk for cardiovascular events, guide therapy, and add to the understanding of plaque biology in human patients

Applications of Medical Physics

Applications of Medical Physics” is a Special Issue of Applied Sciences that has collected original research manuscripts describing cutting-edge physics developments in medicine and their translational applications. Reviews providing updates on the latest progresses in this field are also included. The collection includes a total of 20 contributions by authors from 9 different countries, which cover several areas of medical physics, spanning from radiation therapy, nuclear medicine, radiology, dosimetry, radiation protection, and radiobiology

Magnetic resonance imaging and navigation of ferromagnetic thermoseeds to deliver thermal ablation therapy

Minimally invasive therapies aim to deliver effective treatment whilst reducing off-target burden, limiting side effects, and shortening patient recovery times. Remote navigation of untethered devices is one method that can be used to deliver targeted treatment to deep and otherwise inaccessible locations within the body. Minimally invasive image-guided ablation (MINIMA) is a novel thermal ablation therapy for the treatment of solid tumours, whereby an untethered ferromagnetic thermoseed is navigated through tissue to a target site within the body, using the magnetic field gradients generated by a magnetic resonance imaging (MRI) system. Once at the tumour, the thermoseed is heated remotely using an alternating magnetic field, to induce cell death in the surrounding cancer tissue. The thermoseed is then navigated through the tumour, heating at pre-defined locations until the entire volume has been ablated. The aim of this PhD project is to develop MINIMA through a series of proof-of-concept studies and to assess the efficacy of the three key project components: imaging, navigation, and heating. First, an MR imaging sequence was implemented to track the thermoseeds during navigation and subsequently assessed for precision and accuracy. Secondly, movement of the thermoseeds through a viscous fluid was characterised, by measuring the effect of different navigation parameters. This was followed by navigation experiments performed in ex vivo tissue. To assess thermoseed heating, a series of in vitro experiments were conducted in air, water, and ex vivo liver tissue, before moving onto in vivo experiments in the rat brain and a murine subcutaneous tumour model. These final experiments allowed the extent of cell death induced by thermoseed heating to be determined, in both healthy and diseased tissue respectively

Methods for interventional magnetic resonance imaging

This thesis has as its central aim to demonstrate, develop, discuss and promote new methods and technology for improving interventional low field magnetic resonance imaging. The work addresses problems related to accurate localization of minimally invasive surgical tools by describing novel devices and improvements to prior art techniques, such as optical tracking. In addition to instrument guidance, ablative treatment of liver tumours is discussed in connection with low field temperature measurement and the work describes suitable sequences for qualitative temperature imaging. For instrument localization, a method utilising ex vivo Overhauser enhancement of a catheter like structure was demonstrated. An enhancement factor of 10 was achieved, proving that a substantial signal gain is possible through the use of ex vivo-enhanced liquid. Similarly, a method for biopsy needle tip tracking was developed; where the position of the tip was tracked with a signal from a miniaturized electron spin resonance sample and gradient pulses. At an update rate of 10 samples per second, the accuracy was measured to be better than ±2 mm within a homogeneous sphere of 300 mm. Optical tracking methods concentrated on new indications of use for the developed optical tracking system and associated software: The system was applied to guide the needle 35 times into first sacral root foramina, with a success rate of 97%. It was also used in five bone biopsies, all of which were performed successfully, the samples allowed for a pathologic diagnosis, and the percutaneous procedures could be performed in less than 40 minutes. A new patient tracker device was developed for staged neurosurgical procedures and demonstrated with two patient cases. In the temperature measurement study, spin echo, gradient echo and completely balanced steady-state free precession sequences were optimized for maximal temperature sensitivity and the optimized sequences compared. The steady-state sequence seemed the most promising for the prediction of ablated volume in liver.reviewe

Structural integrity of aortic scaffolds decellularized by sonication decellularization system

Sonication decellularization technique has shown effectiveness to remove all the cellular components by the disruption of the cell membranes and removal of the cell debris to prepare the bioscaffolds. However, it is important to confirm whether this technique does not have a detrimental effect on elastin and collagen in bioscaffolds. The objectives of this study are to evaluate the structural integrity of bioscaffolds using histological staining and quantitatively collagen and elastin measurement. Aortic tissues were sonicated in 0.1% SDS for 10 hours at the frequency of 170 kHz with the power output of 15W and washed in Phosphate Buffer Solution (PBS) for 5 days. Then the sonicated aortic tissues were evaluated by Hematoxylin & Eosin (H&E) staining for cell removal analysis, Verhoeff-van Gieson (VVG) staining for visualizing elastin and Picrosirius Red (PSR) staining for visualizing collagen. The collagen and elastic fibres were semi-quantified by ImageJ software. The results showed that sonication decellularization system can remove all the cellular components while maintaining the structural integrity of elastin and collagen on bioscaffolds. This study indicates that sonication decellularization system could remove all cellular components and maintain the structure of the extracellular matrix