Thomas Sangild Sørensen

Operator-Independent Isotropic Three-Dimensional Magnetic Resonance Imaging for Morphology in Congenital Heart Disease A Validation Study

Background—Operator-independent isotropic 3D MRI may greatly simplify the assessment of complex morphology in congenital heart disease. We sought to evaluate the reliability of this new approach. Methods and Results—In 31 adolescent and adult patients (age, 6 to 42 years; median, 16 years) with congenital heart disease, cardiac morphology was determined with free-breathing (navigator-gated), isotropic, 3D steady-state free-precession (3D SSFP) MRI and independently evaluated by 2 observers. Cardiac diagnoses and multiple distance measurements were compared with conventional MR reference sequences (ie, spin-echo, cine gradient-echo, contrast-enhanced MR angiography) and with echocardiography/cine cardioangiography or surgery. Of the 31 patients, 24 had native congenital heart defects or residual defects after repair that warranted immediate treatment. None of these defects was missed by 3D SSFP. Novel diagnostic issues were discovered in 4 of 31 patients (coronary anomalies, n=3; left juxtaposition of the right atrial appendage in double-outlet right ventricle and transposition of the great arteries, 1). For sizes of valves and vessels, we found minor mean differences of −1.1 to 1.6 mm, with SD ranging from 1.2 to 2.9 mm, demonstrating overall good agreement with standard MRI (Bland-Altman analysis). Interobserver variability of 3D SSFP distance measures was low; mean differences ranged from −1.5 to 1.0 mm, and SD ranged from 0.8 to 2.5 mm. Scatter was lower for extracardiac than intracardiac measures. Conclusions—In adolescents and adults, isotropic 3D SSFP MRI allows reliable assessment of complex cardiac morphology. Distance measurements are accurate and reproducible. Thus, a single operator-independent acquisition may substitute for conventional 2D MRI sequences to accelerate and simplify MR scanning in congenital heart disease.

Gadgetron: An open source framework for medical image reconstruction†

This work presents a new open source framework for medical image reconstruction called the “Gadgetron.” The framework implements a flexible system for creating streaming data processing pipelines where data pass through a series of modules or “Gadgets” from raw data to reconstructed images. The data processing pipeline is configured dynamically at run‐time based on an extensible markup language configuration description. The framework promotes reuse and sharing of reconstruction modules and new Gadgets can be added to the Gadgetron framework through a plugin‐like architecture without recompiling the basic framework infrastructure. Gadgets are typically implemented in C/C++, but the framework includes wrapper Gadgets that allow the user to implement new modules in the Python scripting language for rapid prototyping. In addition to the streaming framework infrastructure, the Gadgetron comes with a set of dedicated toolboxes in shared libraries for medical image reconstruction. This includes generic toolboxes for data‐parallel (e.g., GPU‐based) execution of compute‐intensive components. The basic framework architecture is independent of medical imaging modality, but this article focuses on its application to Cartesian and non‐Cartesian parallel magnetic resonance imaging. Magn Reson Med, 2013.

Four-Dimensional (4D) Flow of the Whole Heart and Great Vessels Using Real-Time Respiratory Self-Gating

Four‐dimensional (4D) flow imaging has been used to study flow patterns and pathophysiology, usually focused on specific thoracic vessels and cardiac chambers. Whole‐heart 4D flow at high measurement accuracy covering the entire thoracic cardiovascular system would be desirable to simplify and improve hemodynamic assessment. This has been a challenge because compensation of respiratory motion is difficult to achieve, but it is paramount to limit artifacts and improve accuracy. In this work we propose a self‐gating technique for respiratory motion‐compensation integrated into a whole‐heart 4D flow acquisition that overcomes these challenges. Flow components are measured in all three directions for each pixel over the complete cardiac cycle, and 1D volume projections are obtained at certain time intervals for respiratory gating in real time during the acquisition. The technique was tested in 15 volunteers, in which stroke volumes (SVs) in the great arteries showed excellent agreement with standard 2D phase‐contrast (PC) scans. In contrast, nongated 4D flow with two averages had substantial disagreement with 2D flow. Applied to patients with congenital cardiac left‐to‐right shunting, the precision of flux data was highly beneficial. The methodology presented here has the potential to allow a complete study of flow pathophysiology of the thoracic cardiovascular system from a single free‐breathing scan. Magn Reson Med, 2009.

Cartesian SENSE and k-t SENSE reconstruction using commodity graphics hardware.

This study demonstrates that modern commodity graphics cards (GPUs) can be used to perform fast Cartesian SENSE and k‐t SENSE reconstruction. Specifically, the SENSE inversion is accelerated by up to two orders of magnitude and is no longer the time‐limiting step. The achieved reconstruction times are now well below the acquisition times, thus enabling real‐time, interactive SENSE imaging, even with a large number of receive coils. The fast GPU reconstruction is also beneficial for datasets that are not acquired in real time. We demonstrate that it can be used for interactive adjustment of regularization parameters for k‐t SENSE in the same way that one would adjust window and level settings. This enables a new way of performing imaging reconstruction, where the user chooses the setting of tunable reconstruction parameters, in real time, depending on the context in which the images are interpreted. Magn Reson Med 59:463–468, 2008.

Acceleration and validation of optical flow based deformable registration for image-guided radiotherapy

Materials and methods. Two registration methods based on optical flow estimation have been programmed to run on a graphics programming unit (GPU). One of these methods by Horn & Schunck is tested on a 4DCT thorax data set with 10 phases and 41 landmarks identified per phase. The other method by Cornelius & Kanade is tested on a series of six 3D cone beam CT (CBCT) data sets and a conventional planning CT data set from a head and neck cancer patient. In each of these data sets 6 landmark points have been identified on the cervical vertebrae and the base of skull. Both CBCT to CBCT and CBCT to CT registration is performed. Results. For the 4DCT registration average landmark error was reduced by deformable registration from 3.5±2.0mm to 1.1±0.6mm. For CBCT to CBCT registration the average bone landmark error was 1.8±1.0mm after rigid registration and 1.6±0.8mm after deformable registration. For CBCT to CT registration errors were 2.2±0.6mm and 1.8±0.6mm for rigid and deformable registration respectively. Using GPU hardware the Horn & Schunck method was accelerated by a factor of 48. The 4DCT registration can be performed in 37seconds. The head and neck cancer patient registration takes 64seconds. Discussion. Compared to image slice thickness, which limits accuracy of landmark point determination, we consider the landmark point accuracy of the registration acceptable. The points identified in the CBCT images do not give a full impression of the result of doing deformable registration as opposed to rigid registration. A larger validation study is being planned in which soft tissue landmarks will facilitate tracking the deformable registration. The acceleration obtained using GPU hardware means that registration can be done online for CBCT.

Retrospective reconstruction of high temporal resolution cine images from real-time MRI using iterative motion correction.

Cardiac function has traditionally been evaluated using breath‐hold cine acquisitions. However, there is a great need for free breathing techniques in patients who have difficulty in holding their breath. Real‐time cardiac MRI is a valuable alternative to the traditional breath‐hold imaging approach, but the real‐time images are often inferior in spatial and temporal resolution. This article presents a general method for reconstruction of high spatial and temporal resolution cine images from a real‐time acquisition acquired over multiple cardiac cycles. The method combines parallel imaging and motion correction based on nonrigid registration and can be applied to arbitrary k‐space trajectories. The method is demonstrated with real‐time Cartesian imaging and Golden Angle radial acquisitions, and the motion‐corrected acquisitions are compared with raw real‐time images and breath‐hold cine acquisitions in 10 (N = 10) subjects. Acceptable image quality was obtained in all motion‐corrected reconstructions, and the resulting mean image quality score was (a) Cartesian real‐time: 2.48, (b) Golden Angle real‐time: 1.90 (1.00–2.50), (c) Cartesian motion correction: 3.92, (d) Radial motion correction: 4.58, and (e) Breath‐hold cine: 5.00. The proposed method provides a flexible way to obtain high‐quality, high‐resolution cine images in patients with difficulty holding their breath. Magn Reson Med, 2012.

Real-Time Reconstruction of Sensitivity Encoded Radial Magnetic Resonance Imaging Using a Graphics Processing Unit

A barrier to the adoption of non-Cartesian parallel magnetic resonance imaging for real-time applications has been the times required for the image reconstructions. These times have exceeded the underlying acquisition time thus preventing real-time display of the acquired images. We present a reconstruction algorithm for commodity graphics hardware (GPUs) to enable real time reconstruction of sensitivity encoded radial imaging (radial SENSE). We demonstrate that a radial profile order based on the golden ratio facilitates reconstruction from an arbitrary number of profiles. This allows the temporal resolution to be adjusted on the fly. A user adaptable regularization term is also included and, particularly for highly undersampled data, used to interactively improve the reconstruction quality. Each reconstruction is fully self-contained from the profile stream, i.e., the required coil sensitivity profiles, sampling density compensation weights, regularization terms, and noise estimates are computed in real-time from the acquisition data itself. The reconstruction implementation is verified using a steady state free precession (SSFP) pulse sequence and quantitatively evaluated. Three applications are demonstrated; real-time imaging with real-time SENSE 1) or k-t SENSE 2) reconstructions, and 3) offline reconstruction with interactive adjustment of reconstruction settings.

Three dimensional three component whole heart cardiovascular magnetic resonance velocity mapping: comparison of flow measurements from 3D and 2D acquisitions

BackgroundTwo-dimensional, unidirectionally encoded, cardiovascular magnetic resonance (CMR) velocity mapping is an established technique for the quantification of blood flow in large vessels. However, it requires an operator to correctly align the planes of acquisition. If all three directional components of velocity are measured for each voxel of a 3D volume through the phases of the cardiac cycle, blood flow through any chosen plane can potentially be calculated retrospectively. The initial acquisition is then more time consuming but relatively operator independent.AimsTo compare the curves and volumes of flow derived from conventional 2D and comprehensive 3D flow acquisitions in a steady state flow model, and in vivo through planes transecting the ascending aorta and pulmonary trunk in 10 healthy volunteers.MethodsUsing a 1.5 T Phillips Intera CMR system, 3D acquisitions used an anisotropic 3D segmented k-space phase contrast gradient echo sequence with a short EPI readout, with prospective ECG and diaphragm navigator gating. The 2D acquisitions used segmented k-space phase contrast with prospective ECG and diaphragm navigator gating. Quantitative flow analyses were performed retrospectively with dedicated software for both the in vivo and in vitro acquisitions.ResultsAnalysis of in vitro data found the 3D technique to have overestimated the continuous flow rate by approximately 5% across the entire applied flow range. In vivo, the 2D and the 3D techniques yielded similar volumetric flow curves and measurements. Aortic flow: (mean ± SD), 2D = 89.5 ± 13.5 ml & 3D = 92.7 ± 17.5 ml. Pulmonary flow: 2D = 98.8 ± 18.4 ml & 3D = 94.9 ± 19.0 ml). Each in vivo 3D acquisition took about 8 minutes or more.ConclusionFlow measurements derived from the 3D and 2D acquisitions were comparable. Although time consuming, comprehensive 3D velocity acquisition could be relatively operator independent, and could potentially yield information on flow through several retrospectively chosen planes, for example in patients with congenital or valvular heart disease.

Two-phase active contour method for semiautomatic segmentation of the heart and blood vessels from MRI images for 3D visualization

The paper presents an active-contour segmentation method for 2D structures in MR images. The method combines two approaches to active contour segmentation, known as balloons and snakes. This makes the method shape independent and accurate. New anti-tangling features were introduced to improve segmentation of very complex object shapes, e.g. the left ventricle with papillary muscles. The method was applied to segment all large structures in the cardiovascular system and its outcome was used for 3D visualization.

GPU accelerated surgical simulators for complex morphology

Surgical training in virtual environments, surgical simulation in other words, has previously had difficulties in simulating deformation of complex morphology in real-time. Even fast spring-mass based systems had slow convergence rates for large models. This paper presents two methods to accelerate a spring-mass system in order to simulate a complex organ such as the heart. Computations are accelerated by taking advantage of modern graphics processing units (GPUs). Two GPU implementations are presented. They vary in their generality of spring connections and in the speedup factor they achieve.