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Modern GPUs are well suited for performing image processing tasks. We utilize their high computational performance and memory bandwidth for image segmentation purposes. We segment cardiac MRI data by means of numerical solution of an anisotropic partial differential equation of the Allen-Cahn type. We implement two different algorithms for solving the equation on the CUDA architecture. One of them is based on the Runge-Kutta-Merson method for the approximation of solutions of ordinary differential equations, the other uses the GMRES method for the numerical solution of systems of linear equations. In our experiments, the CUDA implementations of both algorithms are about 3–9 times faster than corresponding 12-threaded OpenMP implementations.

(Oberhuber T., Suzuki A., Vacata J., Žabka V., “Image segmentation using CUDA implementations of the Runge-Kutta-Merson and GMRES methods“, Journal of Math-for-Industry, 2011, vol. 3, pp. 73–79 [PDF])

The Hough transform is a commonly used algorithm to detect lines and other features in images. It is robust to noise and occlusion, but has a large computational cost. This paper introduces two new implementations of the Hough transform for lines on a GPU. One focuses on minimizing processing time, while the other has an input-data independent processing time. Our results show that optimizing the GPU code for speed can achieve a speed-up over naive GPU code of about 10x. The implementation which focuses on processing speed is the faster one for most images, but the implementation which achieves a constant processing time is quicker for about 20% of the images.

(Gert-Jan van den Braak, Cedric Nugteren, Bart Mesman and Henk Corporaal: “Fast Hough Transform on GPUs: Exploration of Algorithm Trade-offs”. In: Advanced Concepts for Intelligent Vision Systems, Lecture Notes in Computer Science, Vol. 6915, pp.611-622, 2011. [DOI])

CUVI version 0.5 is available for download at http://cuvilib.com and is available for Windows (Win32, x64) with planned support for Linux and Mac.

Functional magnetic resonance imaging (fMRI) makes it possible to non-invasively measure brain activity with high spatial resolution. There are however a number of issues that have to be addressed. One is the large amount of spatio-temporal data that needs to be processed. In addition to the statistical analysis itself, several preprocessing steps, such as slice timing correction and motion compensation, are normally applied. The high computational power of modern graphic cards has already successfully been used for MRI and fMRI. Going beyond the first published demonstration of GPU-based analysis of fMRI data, all the preprocessing steps and two statistical approaches, the general linear model (GLM) and canonical correlation analysis (CCA), have been implemented on a GPU. For an fMRI dataset of typical size (80 volumes with 64 x 64 x 22 voxels), all the preprocessing takes about 0.5 s on the GPU, compared to 5 s with an optimized CPU implementation and 120 s with the commonly used statistical parametric mapping (SPM) software. A random permutation test with 10 000 permutations, with smoothing in each permutation, takes about 50 s if three GPUs are used, compared to 0.5 – 2.5 h with an optimized CPU implementation. The presented work will save time for researchers and clinicians in their daily work and enables the use of more advanced analysis, such as non-parametric statistics, both for conventional fMRI and for real-time fMRI.

(Anders Eklund, Mats Andersson, Hans Knutsson: “fMRI Analysis on the GPU – Possibilities and Challenges”, Computer Methods and Programs in Biomedicine, 2011 [DOI])

Parametric statistical methods, such as Z-, t-, and F-values are traditionally employed in functional magnetic resonance imaging (fMRI) for identifying areas in the brain that are active with a certain degree of statistical significance. These parametric methods, however, have two major drawbacks. First, it is assumed that the observed data are Gaussian distributed and independent; assumptions that generally are not valid for fMRI data. Second, the statistical test distribution can be derived theoretically only for very simple linear detection statistics. With non-parametric statistical methods, the two limitations described above can be overcome. The major drawback of non-parametric methods is the computational burden with processing times ranging from hours to days, which so far have made them impractical for routine use in single subject fMRI analysis. In this work, it is shown how the computational power of cost-efficient Graphics Processing Units (GPUs) can be used to speed up random permutation tests. A test with 10 000 permutations takes less than a minute, making statistical analysis of advanced detection methods in fMRI practically feasible. To exemplify the permutation based approach, brain activity maps generated by the General Linear Model (GLM) and Canonical Correlation Analysis (CCA) are compared at the same significance level. During the development of the routines and writing of the paper, 3-4 years of processing time has been saved by using the GPU.

(Anders Eklund, Mats Andersson, Hans Knutsson: “Fast Random Permutation Tests Enable Objective Evaluation of Methods for Single Subject fMRI Analysis”, International Journal of Biomedical Imaging, Article ID 627947, 2011 [Youtube Video] [PDF])

The use of image denoising techniques is an important part of many medical imaging applications. One common application is to improve the image quality of low-dose, i.e. noisy, computed tomography (CT) data. The medical imaging domain has seen a tremendous development during the last decades. It is now possible to collect time resolved volumes, i.e. 4D data, with a number of modalities (e.g. ultrasound (US), CT, magnetic resonance imaging (MRI)). While 3D image denoising previously has been applied to several volumes independently, there has not been much work done on true 4D image denoising, where the algorithm considers several volumes at the same time (and not a single volume at a time). By using all the dimensions, it is for example possible to remove some of the time varying reconstruction artefacts that exist in CT volumes. The problem with 4D image denoising, compared to 2D and 3D denoising, is that the computational complexity increases exponentially. In this paper we describe a novel algorithm for true 4D image denoising, based on local adaptive filtering, and how to implement it on the graphics processing unit (GPU). The algorithm was applied to a 4D CT heart dataset of the resolution 512 x 512 x 445 x 20. The result is that the GPU can complete the denoising in about 25 minutes if spatial filtering is used and in about 8 minutes if FFT based filtering is used. The CPU implementation requires several days of processing time for spatial filtering and about 50 minutes for FFT based filtering. Fast spatial filtering makes it possible to apply the denoising algorithm to larger datasets (compared to if FFT based filtering is used). The short processing time increases the clinical value of true 4D image denoising significantly.

(Anders Eklund, Mats Andersson, Hans Knutsson: “True 4D Image Denoising on the GPU”, International Journal of Biomedical Imaging, Article ID 952819, 2011 [Youtube Video] [PDF])

Many image processing applications use the histogramming algorithm, which fills a set of bins according to the frequency of occurrence of pixel values taken from an input image. Histogramming has been mapped on a GPU prior to this work. Although significant research effort has been spent in optimizing the mapping, we show that the performance and performance predictability of existing methods can still be improved.

In this paper, we present two novel histogramming methods, both achieving a higher performance and predictability than existing methods. We discuss performance limitations for both novel methods by exploring algorithm trade-offs.

The first novel method gives an average performance increase of 33% over existing methods for non-synthetic benchmarks. The second novel method gives an average performance increase of 56% over existing methods and guarantees to be fully data independent. While the second method is specifically designed for Fermi GPU architectures, the first method is also suitable for older architectures.

(Cedric Nugteren, Gert-Jan van den Braak, Henk Corporaal, Bart Mesman: “High performance predictable histogramming on GPUs: exploring and evaluating algorithm trade-offs”, GPGPU-4: Proceedings of the Fourth Workshop on General Purpose Processing on Graphics Processing Units. [DOI] [Paper and Source Code])

We examine the problem of segmenting foreground objects in live video when background scene textures change over time. In particular, we formulate background subtraction as minimizing a penalized instantaneous risk functional yielding a local on-line discriminative algorithm that can quickly adapt to temporal changes. We analyze the algorithms convergence, discuss its robustness to non-stationarity, and provide an efficient non-linear extension via sparse kernels. To accommodate interactions among neighboring pixels, a global algorithm is then derived that explicitly distinguishes objects versus background using maximum a posteriori inference in a Markov random field (implemented via graph-cuts). By exploiting the parallel nature of the proposed algorithms, we develop an implementation that can run efficiently on the highly parallel Graphics Processing Unit (GPU). Empirical studies on a wide variety of datasets demonstrate that the proposed approach achieves quality that is comparable to state-of-the-art off-line methods, while still being suitable for real-time video analysis (75 fps on a mid-range GPU).

(Li Cheng, M. Gong, D. Schuurmans, and T. Caelli: “Real-time Discriminative Background Subtraction”. IEEE Transactions on Image Processing, 2011, to appear. [DOI] [Sources & Info])

• Using a commercial graphical processing unit and the CUDA programming language to accelerate scientific image processing applications by Broussard and Ives
• GPGPU real-time texture analysis framework by Akhloufi et al.
• A parallel implementation of 3D Zernike moment analysis by Berjón et al.
• Visualization assisted by parallel processing by Lange et al.
• GPU color space conversion by Chase and Vondran
• Acceleration of the Retinex algorithm for image restoration by GPGPU/CUDA by Wang and Huang
• Video transcoding using GPU accelerated decoder by Hsu
• Real-time image deconvolution on the GPU by Klosowski and Krishnan
• GPU-completeness: theory and implications by Lin
• A parallel error diffusion implementation on a GPU by Zhang et al.
• Evaluation of CPU and GPU architectures for spectral image analysis algorithms by Fresse et al.
• Real-time 3D flash ladar imaging through GPU data processing by Wong et al.
• Advanced MRI reconstruction toolbox with accelerating on GPU by Wu et al.
• Accelerating image recognition on mobile devices using GPGPU by López et al.
• A GPU accelerated PDF transparency engine by Recker et al.