CUDA optimization strategies for compute- and memory-bound neuroimaging algorithms

Computer Methods and Programs in Biomedicine

Volumn 106, Issue 3, 2012, Pages 175-187

  Lee, Daren ^a   Dinov, Ivo ^a   Dong, Bin ^b   Gutman, Boris ^a   Yanovsky, Igor ^c   Toga, Arthur W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Compute bound; CUDA; Graphics Processing Unit (GPU); Memory bound; Neuroimaging; Performance Optimization

Indexed keywords

COMPUTE-BOUND; CUDA; GRAPHICS PROCESSING UNIT; MEMORY-BOUND; PERFORMANCE OPTIMIZATIONS;

ALGORITHMS; COMPUTER GRAPHICS; COMPUTER GRAPHICS EQUIPMENT; IMAGE RESOLUTION; NEUROIMAGING; OPTIMIZATION; PARALLEL ARCHITECTURES; PROGRAM PROCESSORS; THREE DIMENSIONAL;

MEMORY ARCHITECTURE;

ALGORITHM; ARTICLE; COMPUTER MEMORY; DATA PROCESSING; HUMAN; NEUROIMAGING; PROCESS OPTIMIZATION; THREE DIMENSIONAL IMAGING;

ALGORITHMS; COMPUTER STORAGE DEVICES; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; NEUROIMAGING; TOMOGRAPHY, X-RAY COMPUTED;

EID: 84860250228     PISSN: 01692607     EISSN: 18727565     Source Type: Journal    
DOI: 10.1016/j.cmpb.2010.10.013     Document Type: Article

References (47)

1. Toga A.W., Mazziotta J.C. Brain Mapping: The Methods 2002, Academic Press.
2. Ryoo S., Rodrigues C.I., Baghsorkhi S.S., Stone S.S., Kirk D.B., Hwu W.W. Optimization principles and application performance evaluation of a multithreaded GPU using CUDA. PPoPP Proceedings: 20-23 February 2008, 73-82.
3. Kutter O., Shams R., Navab N. Visualization and GPU-accelerated simulation of medical ultrasound from ct images. Computer Methods and Programs in BioMedicine 2009, 94:250-266.
4. Jacques R., Taylor R., Wong J., McNutt T. Towards real-time radiation therapy: GPU accelerated superposition/convolution. Computer Methods and Programs in BioMedicine 2009, 94:1-8.
5. Stone J.E., Phillips J.C., Freddolino P.L., Hardy D.J., Trabuco L.G., Schulten K. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry 2007, 28:2618-2640.
6. S. Jung, Parallelized pairwise sequence alignment using CUDA on multiple GPUs, BMC Bioinformatics 10 (Suppl. 7) (2009) A3, doi:10.1186/1471-2105-10-S7-A3. URL: http://www.biomedcentral.com/1471-2105/10/S7/A3.
7. Kirk D., Hwu W. Programming Massively Parallel Processors: A Hands-on Approach 2010, Morgan Kaufmann.
8. Shattuck D.W., Mirzaa M., Adisetiyoa V., Hojatkashania C., Salamon G., Narra K.L., Poldrackc R.A., Bilderc R.M., Toga A.W. Construction of a 3d probabilistic atlas of human cortical structures. NeuroImage 2008, 39:1064-1080.
9. MacKenzie-Graham A., Lee E.-F., Dinov I.D., Bota M., Shattuck D.W., Ruffins S., Yuan H., Konstantinidis F., Pitiot A., Ding Y., Hu G., Jacobs R.E., Toga A.W. A multimodal, multidimensional atlas of the c57bl/6j mouse brain. Journal of Anatomy 2004, 2:93-102.
10. Rueckert D., Frangi A., Schnabel J. Automatic construction of 3d statistical deformation models using non-rigid registration. Medical Image Computing and Computer-Assisted Intervention 2001, pp. 77-84.
11. Sowell E.R., Thompson P.M., Mattson S.N., Tessner K.D., Jernigan T.L., Riley E.P.A., Toga A.W. Voxel-based morphometric analyses of the brain in children and adolescents prenatally exposed to alcohol. NeuroReport 2001, 12:515-523.
12. Thompson P.M., Schwartz C., Toga A.W. High-resolution random mesh algorithms for creating a probabilistic 3d surface atlas of the human brain. NeuroImage 1996, 3:19-34.
13. Köhn A., Drexl J., Tietter F., König M., Peitgen H.O. Gpu accelerated image registration in two and three dimensions. Bildverarbeitung fur die Medizin 2006 2006, Springer, Berlin/Heidelberg, pp. 261-265.
14. Khamene A., Chisu R., Wein W., Navab N., Sauer F. A novel projection based approach for medical image registration. BioMedical Image Registration 2006, Springer, Berlin /Heidelberg, pp. 247-256.
15. Vetter C., Guetter C., Xu C., Westermann R. Non-rigid multi-modal registration on the GPU. SPIE Medical Imaging 2007: Image Processing 2007, 555-560. J.P. Pluim, J.M. Reinhardt (Eds.).
16. Ruijters D., ter Haar-Romeny B.M., Suetens P. Efficient GPU-accelerated elastic image registration. Proc. Sixth IASTED International Conference on Biomedical Engineering (BioMed), Innsbruck, Austria 2008, 419-424.
17. Fan Z., Vetter C., Guetter C., Yu D., Westermann R., Kaufman A., Xu C. Optimized GPU implementation of learning-based non-rigid multi-modal registration. Proceedings of SPIE, vol. 6914 2008, 69142Y.
18. Shams R., Barnes N. Speeding up mutual information computation using nvidia CUDA hardware. Proceedings of the 9th Biennial Conference of the Australian Pattern Recognition Society on Digital Image Computing Techniques and Applications 2007, 555-560. IEEE Computer Society Press.
19. Shams R., Sadeghi P., Kennedy R., Hartley R. Parallel computation of mutual information on the GPU with application to real-time registration of 3d medical images. Computer Methods and Programs in Biomedicine 2009, 10.1016/j.cmpb.2009.11.004.
20. Muyan-Ozcelik P., Owens J.D., Xia J., Samant S.S. Fast deformable registration on the GPU: a CUDA implementation of demons. Proceedings of the 2008 International Conference on Computational Science and Its Applications (ICCSA) 2008, 223-233. IEEE Computer Society Press.
21. Shams R., Sadeghi P., Kennedy R.A., Hartley R.I. A survey of medical image registration on multicore and the GPU. IEEE Signal Processing Magazine 2010, 27(2):50-60.
22. Ryoo S., Rodrigues C.I., Stone S.S., Baghsorkhi S.S., Ueng S.Z., Stratton J.A., Hwu W.W. Program optimization space pruning for a multithreaded gpu. Proceedings of the Sixth Annual IEEE/ACM International Symposium on Code Generation and Optimization 2008, 195-204.
23. Jang B., Do S., Pien H., Kaeli D. Architecture-aware optimization targeting multithreaded stream computing. Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, vol. 383 2009, 62-70.
24. nVidia, Santa Clara, CA, CUDA Programming Guide, August 2009.
25. Cuda occupancy calculator [online].
26. Yanovsky I., Thompson P.M., Osher S., Leow A.D. Topology preserving log-unbiased nonlinear image registration: theory and implementation. IEEE Computer Vision and Pattern Recognition 2007, pp. 1-8.
27. Christensen G., Rabbitt R., Miller M. Deformable templates using large deformation kinematics. IEEE Transactions on Image Processing 1996, 5(10):1435-1447.
28. Christensen G., Johnson H. Consistent image registration. IEEE Transactions on Medical Imaging 2001, 20(7):568-582.
29. D'Agostino E., Maes F., Vandermeulen D., Suetens P. A viscous fluid model for multimodal non-rigid image registration using mutual information. Medical Image Analysis 2003, 7:565-575.
30. Rudin L., Osher S., Fatemi E. Nonlinear total variation based noise removal algorithms. Physics D: Nonlinear Phenomena 1992, 60:259-268.
31. Osher S., Burger M., Goldfarb D., Xu J., Yin W. An iterative regularization method for total variation based image restoration. Multiscale Modeling and Simulation 2005, 4:460-489.
32. Burger M., Gilboa G., Osher S., Xu J. Nonlinear inverse scale space methods. Communications in Mathematical Science 2006, 4(1):179-212.
33. Xu J., Osher S. Iterative regularizaiton and nonlinear inverse scale space applied to wavelet based denoising. IEEE Image Proceedings, vol. 16 2007, pp. 534-544.
34. Tomasi C., Manduchi R. Bilateral filtering for gray and color images. Sixth International Conference on Computer Vision 1998, 839-846.
35. Buades A., Coll B., Morel J.-M. On image denoising methods. Multiscale Modeling and Simulation 2005, 4(2):490-530.
36. Buades A., Coll B., Morel J.-M. Neighborhood filters and pde's. Numerische Mathematik 2006, 105(1):1-34.
37. Gilboa G., Osher S. Nonlocal linear image regularization and supervised segmentation. Multiscale Modeling and Simulation 2007, 6(2):595-630.
38. Gilboa G., Osher S. Nonlocal operators with applications to image processing. CAM-Report 2007, pp. 7-23.
39. Kindermann S., Osher S., Jones P.W. Deblurring and denoising of images by nonlocal functionals. Multiscale Modeling and Simulation 2005, 4(4):1091-1115.
40. Clarenz U., Diewald U., Rumpf M. Anisotropic diffusion in surface processing. Proceedings of IEEE Visualization 2000, 397-405. T. Ertl, B. Hamann, A. Varshney (Eds.).
41. Desbrun M., Meyer M., Schröder P., Barr A. Implicit fairing of irregular meshes using diffusion and curvature flow. ACM SIGGRAPH 1999.
42. Desbrun M., Meyer M., Schröder P., Barr A. Anisotropic feature preserving denoising of height fields and bivariate data. Graphics Interface 2000.
43. Hoppe H., DeRose T., Duchamp T., Halstead M., Jin H., McDonald J., Schweitzer J., Stuetzle W. Piecewise smooth surface reconstruction. ACM SIGGRAPH 1994, pp. 295-302.
44. Tasdizen T., Whitaker R., Burchard P., Osher S. Geometric surface processing via normal maps. ACM Transactions on Graphics 2003, 22:1012-1033.
45. Tasdizen T., Whitaker R.T., Burchard P., Osher S. Geometric surface smoothing via anisotropic diffusion of normals. Proceedings of IEEE Visualization 2002, 125-132.
46. Yoshizawa S., Belyaev A., Seidel H.P. Smoothing by example: Mesh denoising by averaging with similarity-based weights. IEEE International Conference on Shape Modeling and Applications 2006, 38-44.
47. Dong B., Ye J., Osher S., Dinov I. Level set based nonlocal surface restoration. SIAM Multiscale Modeling and Simulation 2008, 7:589-598.