Parallelization of Non-Rigid Image Registration

Non-rigid image registration finds use in a wide range of medical applications ranging from diagnostics to minimally invasive image-guided interventions. Automatic non-rigid image registration algorithms are computationally intensive in that they can take hours to register two images. Although hierarchical volume subdivision-based algorithms are inherently faster than other non-rigid registration algorithms, they can still take a long time to register two images. We show a parallel implementation of one such previously reported and well tested algorithm on a cluster of thirty two processors which reduces the registration time from hours to a few minutes. Mutual information (MI) is one of the most commonly used image similarity measures used in medical image registration and also in the mentioned algorithm. In addition to parallel implementation, we propose a new concept based on bit-slicing to accelerate computation of MI on the cluster and, more generally, on any parallel computing platform such as the Graphics processor units (GPUs). GPUs are becoming increasingly common for general purpose computing in the area of medical imaging as they can execute algorithms faster by leveraging the parallel processing power they offer. However, the standard implementation of MI does not map well to the GPU architecture, leading earlier investigators to compute only an inexact version of MI on the GPU to achieve speedup. The bit-slicing technique we have proposed enables us to demonstrate an exact implementation of MI on the GPU without adversely affecting the speedup

Distributed-memory large deformation diffeomorphic 3D image registration

We present a parallel distributed-memory algorithm for large deformation diffeomorphic registration of volumetric images that produces large isochoric deformations (locally volume preserving). Image registration is a key technology in medical image analysis. Our algorithm uses a partial differential equation constrained optimal control formulation. Finding the optimal deformation map requires the solution of a highly nonlinear problem that involves pseudo-differential operators, biharmonic operators, and pure advection operators both forward and back- ward in time. A key issue is the time to solution, which poses the demand for efficient optimization methods as well as an effective utilization of high performance computing resources. To address this problem we use a preconditioned, inexact, Gauss-Newton- Krylov solver. Our algorithm integrates several components: a spectral discretization in space, a semi-Lagrangian formulation in time, analytic adjoints, different regularization functionals (including volume-preserving ones), a spectral preconditioner, a highly optimized distributed Fast Fourier Transform, and a cubic interpolation scheme for the semi-Lagrangian time-stepping. We demonstrate the scalability of our algorithm on images with resolution of up to $1024^3$ on the "Maverick" and "Stampede" systems at the Texas Advanced Computing Center (TACC). The critical problem in the medical imaging application domain is strong scaling, that is, solving registration problems of a moderate size of $256^3$---a typical resolution for medical images. We are able to solve the registration problem for images of this size in less than five seconds on 64 x86 nodes of TACC's "Maverick" system.Comment: accepted for publication at SC16 in Salt Lake City, Utah, USA; November 201

High-Level Programming for Medical Imaging on Multi-GPU Systems Using the SkelCL Library

Application development for modern high-performance systems with Graphics Processing Units (GPUs) relies on low-level programming approaches like CUDA and OpenCL, which leads to complex, lengthy and error-prone programs. In this paper, we present SkelCL – a high-level programming model for systems with multiple GPUs and its implementation as a library on top of OpenCL. SkelCL provides three main enhancements to the OpenCL standard: 1) computations are conveniently expressed using parallel patterns (skeletons); 2) memory management is simplified using parallel container data types; 3) an automatic data (re)distribution mechanism allows for scalability when using multi-GPU systems. We use a real-world example from the field of medical imaging to motivate the design of our programming model and we show how application development using SkelCL is simplified without sacrificing performance: we were able to reduce the code size in our imaging example application by 50% while introducing only a moderate runtime overhead of less than 5%

Microwave imaging techniques for biomedical applications

Microwaves have been considered for medical applications involving the detection of organ movements and changes in tissue water content. More particularly cardiopulmonary interrogation via microwaves has resulted in various sensors monitoring ventricular volume change or movement, arterial wall motion, respiratory movements, pulmonary oedema, etc. In all these applications, microwave sensors perform local measurements and need to be displaced for obtaining an image reproducing the spatial variations of a given quantity. Recently, advances in the area of inverse scattering theory and microwave technology have made possible the development of microwave imaging and tomographic instruments. This paper provides a review of such equipment developed at Suplec and UPC Barcelona, within the frame of successive French-Spanish PICASSO cooperation programs. It reports the most significant results and gives some perspectives for future developments. Firstly, a brief historical survey is given. Then, both technological and numerical aspects are considered. The results of preliminary pre-clinical assessments and in-lab experiments allow to illustrate the capabilities of the existing equipment, as well as its difficulty in dealing with clinical situations. Finally, some remarks on the expected development of microwave imaging techniques for biomedical applications are given.Peer ReviewedPostprint (published version

GPU-based Iterative Cone Beam CT Reconstruction Using Tight Frame Regularization

X-ray imaging dose from serial cone-beam CT (CBCT) scans raises a clinical concern in most image guided radiation therapy procedures. It is the goal of this paper to develop a fast GPU-based algorithm to reconstruct high quality CBCT images from undersampled and noisy projection data so as to lower the imaging dose. For this purpose, we have developed an iterative tight frame (TF) based CBCT reconstruction algorithm. A condition that a real CBCT image has a sparse representation under a TF basis is imposed in the iteration process as regularization to the solution. To speed up the computation, a multi-grid method is employed. Our GPU implementation has achieved high computational efficiency and a CBCT image of resolution 512\times512\times70 can be reconstructed in ~5 min. We have tested our algorithm on a digital NCAT phantom and a physical Catphan phantom. It is found that our TF-based algorithm is able to reconstrct CBCT in the context of undersampling and low mAs levels. We have also quantitatively analyzed the reconstructed CBCT image quality in terms of modulation-transfer-function and contrast-to-noise ratio under various scanning conditions. The results confirm the high CBCT image quality obtained from our TF algorithm. Moreover, our algorithm has also been validated in a real clinical context using a head-and-neck patient case. Comparisons of the developed TF algorithm and the current state-of-the-art TV algorithm have also been made in various cases studied in terms of reconstructed image quality and computation efficiency.Comment: 24 pages, 8 figures, accepted by Phys. Med. Bio