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Register a new userMulti-Node Multi-GPU Diffeomorphic Image Registration for Large-Scale Imaging Problems
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Added by
Andreas Mang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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We present a Gauss-Newton-Krylov solver for large deformation diffeomorphic image registration. We extend the publicly available CLAIRE library to multi-node multi-graphics processing unit (GPUs) systems and introduce novel algorithmic modifications that significantly improve performance. Our contributions comprise ($i$) a new preconditioner for the reduced-space Gauss-Newton Hessian system, ($ii$) a highly-optimized multi-node multi-GPU implementation exploiting device direct communication for the main computational kernels (interpolation, high-order finite difference operators and Fast-Fourier-Transform), and ($iii$) a comparison with state-of-the-art CPU and GPU implementations. We solve a $256^3$-resolution image registration problem in five seconds on a single NVIDIA Tesla V100, with a performance speedup of 70% compared to the state-of-the-art. In our largest run, we register $2048^3$ resolution images (25 B unknowns; approximately 152$times$ larger than the largest problem solved in state-of-the-art GPU implementations) on 64 nodes with 256 GPUs on TACCs Longhorn system.
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3D image registration is one of the most fundamental and computationally expensive operations in medical image analysis. Here, we present a mixed-precision, Gauss--Newton--Krylov solver for diffeomorphic registration of two images. Our work extends the publicly available CLAIRE library to GPU architectures. Despite the importance of image registration, only a few implementations of large deformation diffeomorphic registration packages support GPUs. Our contributions are new algorithms to significantly reduce the run time of the two main computational kernels in CLAIRE: calculation of derivatives and scattered-data interpolation. We deploy (i) highly-optimized, mixed-precision GPU-kernels for the evaluation of scattered-data interpolation, (ii) replace Fast-Fourier-Transform (FFT)-based first-order derivatives with optimized 8th-order finite differences, and (iii) compare with state-of-the-art CPU and GPU implementations. As a highlight, we demonstrate that we can register $256^3$ clinical images in less than 6 seconds on a single NVIDIA Tesla V100. This amounts to over 20$times$ speed-up over the current version of CLAIRE and over 30$times$ speed-up over existing GPU implementations.
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 TACCs Maverick system.
With widespread advances in machine learning, a number of large enterprises are beginning to incorporate machine learning models across a number of products. These models are typically trained on shared, multi-tenant GPU clusters. Similar to existing cluster computing workloads, scheduling frameworks aim to provide features like high efficiency, resource isolation, fair sharing across users, etc. However Deep Neural Network (DNN) based workloads, predominantly trained on GPUs, differ in two significant ways from traditional big data analytics workloads. First, from a cluster utilization perspective, GPUs represent a monolithic resource that cannot be shared at a fine granularity across users. Second, from a workload perspective, deep learning frameworks require gang scheduling reducing the flexibility of scheduling and making the jobs themselves inelastic to failures at runtime. In this paper we present a detailed workload characterization of a two-month long trace from a multi-tenant GPU cluster in a large enterprise. By correlating scheduler logs with logs from individual jobs, we study three distinct issues that affect cluster utilization for DNN training workloads on multi-tenant clusters: (1) the effect of gang scheduling and locality constraints on queuing, (2) the effect of locality on GPU utilization, and (3) failures during training. Based on our experience running a large-scale operation, we provide design guidelines pertaining to next-generation cluster schedulers for DNN training workloads.
In this article we study the problem of thoracic image registration, in particular the estimation of complex anatomical deformations associated with the breathing cycle. Using the intimate link between the Riemannian geometry of the space of diffeomorphisms and the space of densities, we develop an image registration framework that incorporates both the fundamental law of conservation of mass as well as spatially varying tissue compressibility properties. By exploiting the geometrical structure, the resulting algorithm is computationally efficient, yet widely general.
Image registration plays an important role in medical image analysis. Conventional optimization based methods provide an accurate estimation due to the iterative process at the cost of expensive computation. Deep learning methods such as learn-to-map are much faster but either iterative or coarse-to-fine approach is required to improve accuracy for handling large motions. In this work, we proposed to learn a registration optimizer via a multi-scale neural ODE model. The inference consists of iterative gradient updates similar to a conventional gradient descent optimizer but in a much faster way, because the neural ODE learns from the training data to adapt the gradient efficiently at each iteration. Furthermore, we proposed to learn a modal-independent similarity metric to address image appearance variations across different image contrasts. We performed evaluations through extensive experiments in the context of multi-contrast 3D MR images from both public and private data sources and demonstrate the superior performance of our proposed methods.
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