BOLD fMRI Simulation

Background: Brain functional magnetic resonance imaging (fMRI) is sensitive to changes in blood oxygenation level dependent (BOLD) brain magnetic states. The fMRI scanner produces a complex-valued image, but the calculation of the original BOLD magnetic source is not a mathematically tractable problem. We conduct numeric simulations to understand the BOLD fMRI model

Motion Robust Magnetic Susceptibility and Field Inhomogeneity Estimation Using Regularized Image Restoration Techniques for fMRI

In functional MRI, head motion may cause dynamic nonlinear field-inhomogeneity changes, especially with large out-of-plane rotations. This may lead to dynamic geometric distortion or blurring in the time series, which may reduce activation detection accuracy. The use of image registration to estimate dynamic field inhomogeneity maps from a static field map is not sufficient in the presence of such rotations. This paper introduces a retrospective approach to estimate magnetic susceptibility induced field maps of an object in motion, given a static susceptibility induced field map and the associated object motion parameters. It estimates a susceptibility map from a static field map using regularized image restoration techniques, and applies rigid body motion to the former. The dynamic field map is then computed using susceptibility voxel convolution. The method addresses field map changes due to out-of-plane rotations during time series acquisition and does not involve real time field map acquisitions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85944/1/Fessler233.pd

Advanced interfaces for biomedical engineering applications in high- and low field NMR/MRI

Das zentrale Thema dieser Dissertation ist die Magnetresonanz(MR)-Sicherheit und MR-Kompatibilität von Bauelementen. Der Öffentlichkeit bekannt ist diese Thematik im Zusammenhang mit kommerziellen Implantaten. Die Gefahren, die sich aus den Wechselwirkungen zwischen dem MR-Tomografen (MRT) und dem Implantat ergeben, hindern viele Patienten daran, eine Untersuchung mittels MRT durchführen zu lassen. MR-Kompatibilität spielt jedoch nicht nur beim Design und der Kennzeichnung von Implantaten eine wichtige Rolle, sondern auch bei der Entwicklung von Bauelementen für die MR-Hardware. Beide Themen, Implantatinteraktionen und Hardware-Design, bilden fundamentale Aspekte dieser Arbeit. Der erste Teil befasst sich mit MRT-Wechselwirkungen von Implantaten. Die Ergebnisse einer umfangreichen Literaturrecherche zeigen, dass dringend belastbare Daten benötigt werden, um die durch MRT ausgelösten Schwingungen von Implantaten besser verstehen zu können. Dies gilt insbesondere für Vibrationen in viskoelastischen Umgebungen wie dem Gehirn. Im Rahmen dieser Arbeit wird ein neuartiges Messsystem vorgestellt, mit dem sich Schwingungen bei Standard-MRT-Aufnahmen und mit hoher Genauigkeit quantitativ messen lassen. Durch die Verwendung einer amplituden- und frequenzgesteuerten externen Stromversorgung werden die Übertragungsfunktionen implantatartiger Strukturen in viskoelastischen Umgebungen präzise bestimmt. Basierend auf den erfassten Daten wird eine Korrelation zwischen den resultierenden Schwingungsamplituden und den Zeitparametern der Aufnahmesequenz hergestellt und experimentell verifiziert. Eine wichtige Erkenntnis ist, dass die untersuchten Strukturen ein unterdämpftes Verhalten zeigen und damit resonant schwingen können. Darüber hinaus wird eine neue Kennzahl eingeführt, anhand derer die Wechselwirkung des Implantats auf Vibrationen klassifiziert werden können. Die Kennzahl gibt das normierte induzierte Drehmoment an, und ermöglicht eine einfache Berechnung des maximal zu erwartenden Drehmomoments auf jedem MRT-System. Somit können die zu erwartenden Maximalamplituden unkompliziert und für jedes System direkt ermittelt werden. Eine anderes Forschungsgebiet, die in-situ-Kernspinspektroskopie und -MRT von biologischen Untersuchungsobjekten im Hochfeld, erfordert eine neuartige MR-Messsonde sowie verbesserte MR-kompatible Substrate für die Zellkultivierung. Eine MR-Sonde mit flexibler Schnittstelle wurde entwickelt. Die endgültige Version ist mit zwei HF-Kanälen und einer Gradientenschnittstelle für flüssiggekühlte Gradienten ausgestattet. Ein Leistungsbewertung wurde mittels Standard-NMR/MRT-Experimenten durchgeführt, die eine Linienbreite von 0,5 Hz und ein mit kommerziellen Messsystem vergleichbares Signal-Rausch-Verhältnis ergaben. Der Vorteil liegt in dem integrierten Durchführungssystem innerhalb des mechanischen Rahmens. Dies bietet eine einfache Methode, zur spezifischen Erweiterung der Messsonde unter Verwendung zusätzlicher elektrischer, optischer und fluidischer Versorgungsleitungen. Auf dieser Basis können spezifische, komplexe experimentelle Hochfeld-NMR/MRT-Aufbauten in kurzer Zeit realisiert werden, ohne Bedarf nach maßgeschneiderten, teuren Sonden. Als Referenz werden zwei Messaufbauen präsentiert, bei ersterem wird die Sonde für ein Öl-Wasser-Fluidikexperiment und bei dem zweitem, in einem wasserstoffbasierten Hyperpolarisationsexperiment eingesetzt. Darüber hinaus wird ein neuartiges, MR-kompatibles 3D-Zellsubstrat basierend auf Kohlenstoff vorgestellt, das erfolgreich auf Zellwachstum und MR-Bildgebung getestet wurde. Die MRT dient des Weiteren als Analysewerkzeug, um die Erhaltung der Morphologie während der Pyrolyse zu untersuchen und zu bestätigen. Das Herstellungsprotokoll ist auf andere Vorläuferpolymere anwendbar, die den Weg zu einer Vielzahl von lithografisch strukturierten 3D-Gerüsten ebnen

Segmentation of neuroanatomy in magnetic resonance images

Segmentation in neurological Magnetic Resonance Imaging (MRI) is necessary for volume measurement, feature extraction and for the three-dimensional display of neuroanatomy. This thesis proposes several automated and semi-automated methods which offer considerable advantages over manual methods because of their lack of subjectivity, their data reduction capabilities, and the time savings they give. Work has concentrated on the use of dual echo multi-slice spin-echo data sets in order to take advantage of the intrinsically multi-parametric nature of MRI. Such data is widely acquired clinically and segmentation therefore does not require additional scans. The literature has been reviewed. Factors affecting image non-uniformity for a modem 1.5 Tesla imager have been investigated. These investigations demonstrate that a robust, fast, automatic three-dimensional non-uniformity correction may be applied to data as a pre-processing step. The merit of using an anisotropic smoothing method for noisy data has been demonstrated. Several approaches to neurological MRI segmentation have been developed. Edge-based processing is used to identify the skin (the major outer contour) and the eyes. Edge-focusing, two threshold based techniques and a fast radial CSF identification approach are proposed to identify the intracranial region contour in each slice of the data set. Once isolated, the intracranial region is further processed to identify CSF, and, depending upon the MRI pulse sequence used, the brain itself may be sub-divided into grey matter and white matter using semiautomatic contrast enhancement and clustering methods. The segmentation of Multiple Sclerosis (MS) plaques has also been considered. The utility of the stack, a data driven multi-resolution approach to segmentation, has been investigated, and several improvements to the method suggested. The factors affecting the intrinsic accuracy of neurological volume measurement in MRI have been studied and their magnitudes determined for spin-echo imaging. Geometric distortion - both object dependent and object independent - has been considered, as well as slice warp, slice profile, slice position and the partial volume effect. Finally, the accuracy of the approaches to segmentation developed in this thesis have been evaluated. Intracranial volume measurements are within 5% of expert observers' measurements, white matter volumes within 10%, and CSF volumes consistently lower than the expert observers' measurements due to the observers' inability to take the partial volume effect into account

Recommended Implementation of Quantitative Susceptibility Mapping for Clinical Research in The Brain: A Consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group

This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available give rise to the need in the neuroimaging community for guidelines on implementation. This article describes relevant considerations and provides specific implementation recommendations for all steps in QSM data acquisition, processing, analysis, and presentation in scientific publications. We recommend that data be acquired using a monopolar 3D multi-echo GRE sequence, that phase images be saved and exported in DICOM format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields should be removed within the brain mask using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of whole brain as a region of interest in the analysis, and QSM results should be reported with - as a minimum - the acquisition and processing specifications listed in the last section of the article. These recommendations should facilitate clinical QSM research and lead to increased harmonization in data acquisition, analysis, and reporting

New Technology and Techniques for Needle-Based Magnetic Resonance Image-Guided Prostate Focal Therapy

The most common diagnosis of prostate cancer is that of localized disease, and unfortunately the optimal type of treatment for these men is not yet certain. Magnetic resonance image (MRI)-guided focal laser ablation (FLA) therapy is a promising potential treatment option for select men with localized prostate cancer, and may result in fewer side effects than whole-gland therapies, while still achieving oncologic control. The objective of this thesis was to develop methods of accurately guiding needles to the prostate within the bore of a clinical MRI scanner for MRI-guided FLA therapy. To achieve this goal, a mechatronic needle guidance system was developed. The system enables precise targeting of prostate tumours through angulated trajectories and insertion of needles with the patient in the bore of a clinical MRI scanner. After confirming sufficient accuracy in phantoms, and good MRI-compatibility, the system was used to guide needles for MRI-guided FLA therapy in eight patients. Results from this case series demonstrated an improvement in needle guidance time and ease of needle delivery compared to conventional approaches. Methods of more reliable treatment planning were sought, leading to the development of a systematic treatment planning method, and Monte Carlo simulations of needle placement uncertainty. The result was an estimate of the maximum size of focal target that can be confidently ablated using the mechatronic needle guidance system, leading to better guidelines for patient eligibility. These results also quantified the benefit that could be gained with improved techniques for needle guidance

Inhomogeneity Correction in High Field Magnetic Resonance Images

Projecte realitzat en col.laboració amb el centre Swiss Federal Institute of Technology (EPFL)Magnetic Resonance Imaging, MRI, is one of the most powerful and harmless ways to study human inner tissues. It gives the chance of having an accurate insight into the physiological condition of the human body, and specially, the brain. Following this aim, in the last decade MRI has moved to ever higher magnetic field strength that allow us to get advantage of a better signal-to-noise ratio. This improvement of the SNR, which increases almost linearly with the field strength, has several advantages: higher spatial resolution and/or faster imaging, greater spectral dispersion, as well as an enhanced sensitivity to magnetic susceptibility. However, at high magnetic resonance imaging, the interactions between the RF pulse and the high permittivity samples, which causes the so called Intensity Inhomogeneity or B1 inhomogeneity, can no longer be negligible. This inhomogeneity causes undesired efects that afects quantitatively image analysis and avoid the application classical intensity-based segmentation and other medical functions. In this Master thesis, a new method for Intensity Inhomogeneity correction at high ¯eld is presented. At high ¯eld is not possible to achieve the estimation and the correction directly from the corrupted data. Thus, this method attempt the correction by acquiring extra information during the image process, the RF map. The method estimates the inhomogeneity by the comparison of both acquisitions. The results are compared to other methods, the PABIC and the Low-Pass Filter which try to correct the inhomogeneity directly from the corrupted data

Realistic simulation of artefacts in diffusion MRI for validating post-processing correction techniques

AbstractIn this paper we demonstrate a simulation framework that enables the direct and quantitative comparison of post-processing methods for diffusion weighted magnetic resonance (DW-MR) images. DW-MR datasets are employed in a range of techniques that enable estimates of local microstructure and global connectivity in the brain. These techniques require full alignment of images across the dataset, but this is rarely the case. Artefacts such as eddy-current (EC) distortion and motion lead to misalignment between images, which compromise the quality of the microstructural measures obtained from them. Numerous methods and software packages exist to correct these artefacts, some of which have become de-facto standards, but none have been subject to rigorous validation. In the literature, improved alignment is assessed using either qualitative visual measures or quantitative surrogate metrics. Here we introduce a simulation framework that allows for the direct, quantitative assessment of techniques, enabling objective comparisons of existing and future methods. DW-MR datasets are generated using a process that is based on the physics of MRI acquisition, which allows for the salient features of the images and their artefacts to be reproduced. We apply this framework in three ways. Firstly we assess the most commonly used method for artefact correction, FSL's eddy_correct, and compare it to a recently proposed alternative, eddy. We demonstrate quantitatively that using eddy_correct leads to significant errors in the corrected data, whilst eddy is able to provide much improved correction. Secondly we investigate the datasets required to achieve good correction with eddy, by looking at the minimum number of directions required and comparing the recommended full-sphere acquisitions to equivalent half-sphere protocols. Finally, we investigate the impact of correction quality by examining the fits from microstructure models to real and simulated data

Coupling solid and fluid stresses with brain tumour growth and white matter tract deformations in a neuroimaging-informed model

Brain tumours are among the deadliest types of cancer, since they display a strong ability to invade the surrounding tissues and an extensive resistance to common therapeutic treatments. It is therefore important to reproduce the heterogeneity of brain microstructure through mathematical and computational models, that can provide powerful instruments to investigate cancer progression. However, only a few models include a proper mechanical and constitutive description of brain tissue, which instead may be relevant to predict the progression of the pathology and to analyse the reorganization of healthy tissues occurring during tumour growth and, possibly, after surgical resection. Motivated by the need to enrich the description of brain cancer growth through mechanics, in this paper we present a mathematical multiphase model that explicitly includes brain hyperelasticity. We find that our mechanical description allows to evaluate the impact of the growing tumour mass on the surrounding healthy tissue, quantifying the displacements, deformations, and stresses induced by its proliferation. At the same time, the knowledge of the mechanical variables may be used to model the stress-induced inhibition of growth, as well as to properly modify the preferential directions of white matter tracts as a consequence of deformations caused by the tumour. Finally, the simulations of our model are implemented in a personalized framework, which allows to incorporate the realistic brain geometry, the patient-specific diffusion and permeability tensors reconstructed from imaging data and to modify them as a consequence of the mechanical deformation due to cancer growth

Optimization of a boundary element approach to electromagnet design with application to a host of current problems in Magnetic Resonance Imaging

Magnetic resonance imaging (MRI) has proven to be a valuable methodological approach in both basic research and clinical practice. However, significant hardware advances are still needed in order to further improve and extend the applications of the technique. The present dissertation predominantly addresses gradient and shim coil design (sub-systems of the MR system). A design study to investigate gradient performance over a set of surface geometries ranging in curvature from planar to a full cylinder using the boundary element (BE) method is presented. The results of this study serve as a guide for future planar and pseudo-planar gradient systems for a range of applications. Additions to the BE method of coil design are developed, including the direct control of the magnetic field uniformity produced by the final electromagnet and the minimum separation between adjacent wires in the final design. A method to simulate induced eddy currents on thin conducting surfaces is presented. The method is used to predict the time-dependent decay of eddy currents induced on a cylindrical copper bore within a 7 T MR system and the induced heating on small conducting structures; both predictions are compared against experiment. Next, the method is extended to predict localized power deposition and the spatial distribution of force due to the Lorentz interaction of the eddy current distribution with the main magnetic field. New methods for the design of actively shielded electromagnets are presented and compared with existing techniques for the case of a whole-body transverse gradient coil. The methods are judged using a variety of shielding performance parameters. A novel approach to eliminate the interactions between the MR gradient system and external, non-MR specific, active devices is presented and its feasibility is discussed. A completely new approach to shimming is presented utilizing a network of current pathways that can be adaptively changed on a subject-by-subject basis and dynamically controlled. The potential benefits of the approach are demonstrated using computer simulations and a prototype coil is constructed and tested as a proof-of-principle