Vessel segmentation for time resolved phase contrast MRI

Quantication of cardiovascular flow and blood volumes are useful tools in diagnosing cardiovascular disease such as congenital heart defects and different kinds of valve leakage. Medical imaging techniques enables non-invasive analysis of anatomy and physiology. In order to perform flow quantification from medical image sequences, the boundaries of the vessels of interest are usually delineated manually by medical professionals. This is a time consuming process and the result depends, to a high degree, on user experience. This thesis presents an automated vessel segmentation method for the main vessels around the heart from velocity encoded Magnetic Resonance Imaging sequences. The proposed method only require a manual delineation in one image. The algorithm is based on an active contour, using the Euler-Lagrange equation together with internal and external forces designed from a set of fundamental assumptions regarding vessel shape and behaviour. More specically, constraints were applied to the geometrical shape and elasticity of a vessel. Validation of the method was performed by comparing the detected stroke volume with manual delineation, and also by measuring the segmentation overlapping of the two methods. On a test set of 20 patients, 19 resulted in excellent segmentation agreement with manual delineations, with a mean Dice coefficient over 0.8. However, performance instability was observed when changing the values of two algorithm parameters, and one of the patients in the set constantly resulted in segmentation failure for all tested parameter combinations. The relative variability in stroke volume between the proposed algorithm and manual delineations was, at best, 6 +- 3.6%. This is comparable to the interobserver variability from a previous physiological study 1 of 3 +- 4%, which indicates the potential of the suggested method if improvements in robustness and stability is implemented

Validation of Phase Contrast Flow Quantification and Relaxometry for Cardiovascular Magnetic Resonance Imaging

Quantitative imaging, where every pixel of an image represents a physical quantity (e.g. timeor velocity) is being increasingly used in the field of diagnostic radiology and has potential toenhance medical diagnosis. Quantitative methods for Magnetic Resonance Imaging (MRI)enables measurements of velocity and flow using a technique called Phase Contrast MagneticResonance (PC-MR), and different time constants of the magnetic resonance signal can bemeasured to characterize different tissue types such as muscle and fat in MR images using atechnique called magnetic resonance relaxometry.One of the first clinical applications of MR relaxometry was to estimate iron load indifferent organs noninvasively by measuring the time constant called T2*. Patients sufferingfrom iron load disease are at risk of developing organ failure due to iron overload. Ironchelate therapy has been shown to reduce chronic iron overload but it is toxic and has beenlinked to renal failure at high doses. MRI T2* measurements can be used to effectively tailorchelate therapy for patients with iron load disease, thereby reducing mortality of the disease.Several methods for calculating T2* from MRI images are currently being used, each withits own advantages and disadvantages. Different MRI vendors generally use slightly differentmethods. Further, some methods are mainly suitable for cases with moderate to normal ironload while other methods are more suitable for cases with severe iron load.For other clinical applications of MR relaxometry the MR time constants called T1 andT2 are measured. For example, T1 measurements before and after administration of a certainMRI contrast agent makes it possible to determine the extracellular volume in different partsof the heart muscle which can be used to examine damages to the heart muscle after a heartattack. T2 measurements can for example be used to detect edema in the heart muscle andto determine blood oxygen saturation noninvasively. Several methods exist for T1 and T2calculation from MRI images and software tools that can be used to calculate T1 and T2values could be of help to standardize methodology in the clinics. A previous software for T1and T2 analysis exist but it is designed to be used for research only.The latest MR relaxometry methods often use computer simulations of MR physics togetherwith MR images to enable measurement of several MR time constants at the sametime or to increase the accuracy of each measurement. These techniques show great promisein advancing the research field of MRI but current methods require state of the art measurementtechniques which can only be implemented on high-end MRI scanners, limiting wide Imaging clinical use. Phase Contrast Magnetic Resonance (PC-MR) can be used to measure velocity in each pixel of an MRI image and have been used for many years as the reference standard for noninvasive measurements of blood flow. In order to measure the total net flow in a blood vessel over a heartbeat, the vessel of interest has to be delineated in a time-resolved PC-MR image series usually containing 15-35 images. Manual vessel delineation in these images is time consuming and requires user experience for accurate results. Semi-automatic delineation methods based on image analysis have reduced the amount of required user input and the total time of analysis for PC-MR flow measurements. However, currently existing semi-automatic methods often need manual corrections from the user. Non-invasive flow and blood velocity measurements in the fetal cardiovascular system by MRI is a promising alternative to doppler ultrasound for diagnosing disease such as congenital heart defects and intra-uterine growth restriction. Conventional PC-MR flow measurements require an ECG-recording during the MRI scan which is used to sort the collected MRI data to form a time-resolved video over a heartbeat, a process called retrospective image gating. The lack of a usable ECG by surface electrodes for fetal imaging requires alternative image gating techniques. Metric Optimized Gating (MOG) is a previously published image gating technique which does not require a fetal ECG recording. MOG together with PC-MR flow measurements (MOG PC-MR) has demonstrated reproducibility for fetal imaging in studies from one research center. However, MOG PC-MR flow measurements have not been validated for a range of flow rates or a range of peak velocity. This dissertation investigates existing and newly developed MR relaxometry and PC-MR measurement methods with the purpose of evaluating clinical applicability. In Study I a new vendor-independent T2* calculation method was validated over the range of clinically relevant T2* values in phantom experiments. Invivo T2* measurements using the proposed method were in good agreement with T2* measurements using a vendorspecific T2* method in the heart and liver of patients with known or suspected iron load disease. In Study II a vendor-independent software for T1 and T2 analysis was validated in phantom experiments. In Study III a new MR-relaxometry method called SQUAREMR, which was applied to a previously introduced and widely available T1 measurement technique (MOLLI), was shown to provide improved T1 measurement accuracy in phantom experiments. In Study IV a new semi-automatic delineation method for PC-MR flow measurements which uses a database of manual vessel delineations to control the shape of the delineation was validated in a pulsatile flow phantom experiment and showed good agreement with manual delineations in invivo PC-MR images of the ascending aorta and main pulmonary artery. Finally, in Study V MOG PC-MR showed good agreement with conventional PC-MR in a pulsatile flow phantom experiment except for cases with low Velocity to Noise Ratio (VNR), which resulted in underestimation of peak velocity and overestimation of flow which warrants optimization of the PC-MR measurement to individual fetal vessels for accurate MOG PC MR fetal flow measurements

Independent validation of four-dimensional flow MR velocities and vortex ring volume using particle imaging velocimetry and planar laser-Induced fluorescence. : Validation of 4D Flow using PIV and PLIF

PURPOSE:This study aimed to: (i) present and characterize a phantom setup for validation of four-dimensional (4D) flow using particle imaging velocimetry (PIV) and planar laser-induced fluorescence (PLIF); (ii) validate 4D flow velocity measurements using PIV; and (iii) validate 4D flow vortex ring volume (VV) using PLIF.METHODS:A pulsatile pump and a tank with a 25-mm nozzle were constructed. PIV measurements (1.5 × 1.5 mm pixels, temporal resolution 10 ms) were obtained on two occasions. The 4D flow (3 × 3 × 3 mm voxels, temporal resolution 50 ms) was acquired using SENSE = 2. VV was quantified using PLIF and 4D flow.RESULTS:PIV showed excellent day-to-day stability (R(2) = 0.99, bias -0.04 ± 0.72 cm/s). The 4D flow mean velocities agreed well with PIV (R(2) = 0.95, bias 0.16 ± 2.65 cm/s). Peak velocities in 4D flow were underestimated by 7-18% compared with PIV (y = 0.79x + 2.7, R(2) = 0.96, -12 ± 5%). VV showed excellent agreement between PLIF and 4D flow (R(2) = 0.99, 2.4 ± 1.5 mL).CONCLUSION:This study shows: (i) The proposed phantom enables reliable validation of 4D flow. (ii) 4D flow velocities show good agreement with PIV, but peak velocities were underestimated due to low spatial and temporal resolution. (iii) Vortex ring volume (VV) can be quantified using 4D flow

Parallel simulations for QUAntifying RElaxation magnetic resonance constants (SQUAREMR): an example towards accurate MOLLI T1 measurements.

T1 mapping is widely used today in CMR, however, it underestimates true T1 values and its measurement error is influenced by several acquisition parameters. The purpose of this study was the extraction of accurate T1 data through the utilization of comprehensive, parallel Simulations for QUAntifying RElaxation Magnetic Resonance constants (SQUAREMR) of the MOLLI pulse sequence on a large population of spins with physiologically relevant tissue relaxation constants

Fetal iGRASP cine CMR assisting in prenatal diagnosis of complicated cardiac malformation with impact on delivery planning

Limited visualisation of the fetal heart and vessels by fetal ultrasound due to suboptimal fetal position, patient habitus and skeletal calcification may lead to missed diagnosis, overdiagnosis and parental uncertainty. Counseling and delivery planning may in those cases also be tentative. The recent fetal cardiac magnetic resonance (CMR) reconstruction method utilising tiny golden angle iGRASP (iterative Golden-angle RAdial Sparse Parallel MRI) allows for cine imaging of the fetal heart for use in clinical practice. This case describes an unbalanced common atrioventricular canal where limited ultrasound image quality and visibility of the aortic arch precluded confirming or ruling out presence of a ventricular septal defect. Need of prostaglandins or neonatal intervention was thus uncertain. Cardiovascular magnetic resonance imaging confirmed ultrasound findings and added value by ruling out a significant ventricular septal defect and diagnosing arch hypoplasia. This confirmed the need of patient relocation for delivery at a paediatric cardiothoracic surgery centre and prostaglandins could be initiated before the standard postnatal ultrasound. The applied CMR method can thus improve diagnosis of complicated fetal cardiac malformation and has direct clinical impact. This article is protected by copyright. All rights reserved

Validation of T1 and T2 algorithms for quantitative MRI : Performance by a vendor-independent software

Background: Determination of the relaxation time constants T1 and T2 with quantitative magnetic resonance imaging is increasingly used for both research and clinical practice. Recently, groups have been formed within the Society of Cardiovascular Magnetic Resonance to address issues with relaxometry. However, so far they have avoided specific recommendations on methodology due to lack of consensus and current evolving research. Standardised widely available software may simplify this process. The purpose of the current study was to develop and validate vendor-independent T1 and T2 mapping modules and implement those in the versatile and widespread software Segment, freely available for research and FDA approved for clinical applications. Results: The T1 and T2 mapping modules were developed and validated in phantoms at 1.5T and 3T with reference standard values calculated from reference pulse sequences using the Nelder-Mead Simplex optimisation method. The proposed modules support current commonly available MRI pulse sequences and both 2- and 3-parameter curve fitting. Images acquired in patients using three major vendors showed vendor-independence. Bias and variability showed high agreement with T1 and T2 reference standards for T1 (range 214-1752ms) and T2 (range 45-338ms), respectively. Conclusions: The developed and validated T1 and T2 mapping and quantification modules generated relaxation maps from current commonly used MRI sequences and multiple signal models. Patient applications showed usability for three major vendors