High performance volume-of-intersection projectors for 3D-PET image reconstruction based on polar symmetries and SIMD vectorisation. (18th November 2015)

• Record Type: Journal Article
• Authors: Scheins, J J; Vahedipour, K; Pietrzyk, U; Shah, N J
• Is Part Of: Physics in medicine & biology. Volume 60:Number 24(2015:Dec.)
• Page Start: 9349
• Page End: 9375
• Publication Date: 2015-11-18
• Subjects: PET -- iterative reconstruction -- system response matrix -- symmetries -- SIMD -- vectorisation; Biophysics -- Periodicals; Medical physics -- Periodicals; 610.153
• DOI: 10.1088/0031-9155/60/24/9349
• Languages: English
• ISSNs: 0031-9155

Abstract

Abstract: For high-resolution, iterative 3D PET image reconstruction the efficient implementation of forward-backward projectors is essential to minimise the calculation time. Mathematically, the projectors are summarised as a system response matrix (SRM) whose elements define the contribution of image voxels to lines-of-response (LORs). In fact, the SRM easily comprises billions of non-zero matrix elements to evaluate the tremendous number of LORs as provided by state-of-the-art PET scanners. Hence, the performance of iterative algorithms, e.g. maximum-likelihood-expectation-maximisation (MLEM), suffers from severe computational problems due to the intensive memory access and huge number of floating point operations. Here, symmetries occupy a key role in terms of efficient implementation. They reduce the amount of independent SRM elements, thus allowing for a significant matrix compression according to the number of exploitable symmetries. With our previous work, the PET REconstruction Software TOolkit (PRESTO), very high compression factors (>300) are demonstrated by using specific non-Cartesian voxel patterns involving discrete polar symmetries. In this way, a pre-calculated memory-resident SRM using complex volume-of-intersection calculations can be achieved. However, our original ray-driven implementation suffers from addressing voxels, projection data and SRM elements in disfavoured memory access patterns. As a consequence, a rather limited numerical throughput is observed due to the massive waste of memory bandwidth and inefficient usage of cache respectively. In this work, an advantageous symmetry-driven evaluation of the forward-backward projectors is proposed to overcome these inefficiencies. The polar symmetries applied in PRESTO suggest a novel organisation of image data and LOR projection data in memory to enable an efficient single instruction multiple data vectorisation, i.e. simultaneous use of any SRM element for symmetric LORs. In addition, the calculation time is further reduced by using simultaneous multi-threading (SMT). A global speedup factor of 11 without SMT and above 100 with SMT has been achieved for the improved CPU-based implementation while obtaining equivalent numerical results.