Abstract
In this paper, we proposed a method for accelerating brain extraction computations from cerebral MRI volume using compute unified device architecture (CUDA) based on multi-core graphic processing units (GPU). This algorithm is based on the well-known brain extraction method—Brain Extraction Tool (BET). In order to significantly reduce the computational time for real-time processing, the algorithm was performed in a parallel way by assigning one thread in GPU to calculate the new position of one vertex on the brain surface and all the vertices on the brain surface on one slice are processed in the same thread block, thus all the positions of the vertices on the brain’s surface can be updated in the same time. Experiments showed the computational time of this parallel method was less than one second and much less than that of normal BET. A slice-by-slice way was also used to improve the accuracy of our algorithm, and both the result and consuming time are desirable.
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References
Smith SM (2002) Fast robust automated brain extraction. Hum Brain Mapp 17(3):143–155
Shattuck DW, Sandor-Leahy SR, Schaper KA, Rottenberg DA, Leahy RM (2001) Magnetic resonance image tissue classification using a partial volume model. Neuroimage 13(5):856–876
Huang A, Abugharbieh R, Tam R, Traboulsee A (2006) MRI brain extraction with combined expectation maximization and geodesic active contours. In: Proceedings of 2006 IEEE symposium on signal processing and information technology, Vancouver, Canada, pp 107–111
Zhuang AH, Valentino DJ, Togaa AW (2006) Skull-stripping magnetic resonance brain images using a model-based level set. NeuroImage 32(1):79–92
Pan L, Gu L, Xu J (2008) Implementation of medical image segmentation in CUDA. Int Conf Technol Appl Biomed 82–85
Vetter C, Guetter C, Xu C, Westermann R (2007) Non-rigid multi-modal registration on the GPU. Medical Imaging 2007: Image Processing, SPIE, vol 6512, March
Chen S, Qin J, Xie Y, Zhao J, Pang W-M, Heng P-A (2009) CUDA acceleration and algorithm refinement for volume image registration. In: 2009 International conference on future biomedical information engineering
Mueller K, Xu F, Neophytou N (2007) Why do commodity graphics hardware boards (GPUs) work so well for acceleration of computed tomography? In: SPIE electronic imaging 2007, computational imaging V Keynote
Sharp GC, Kandasamy N, Singh H (2007) GPU-based streaming architectures for fast cone-beam CT image reconstruction and Demons deformable registration. Phys Med Biol
Stone S, Haldar J, Tsao S, Hwu W, Liang Z, Sutton B (2008) Accelerating advanced MRI reconstructions on GPUs. ACM Frontiers in Computing, Ischia
Jiang S, Yang S, Chen Z, Chen W (2009) Automatic extraction of brain from cerebral MR image based on improved BET method. In: 2009 2nd International conference on biomedical engineering and information, pp 132–135
Jiang S, Chen Z, Wang Y, Yang S, Chen W (2010) CUDA-based real-time brain extraction method from cerebral MRI volume. In: IASTED technology conferences
Dhanasekaran B, Rubin N (2011) A new method for GPU based irregular reductions and its application to k-means clustering. In: ASPLOS workshop on general purpose processing on graphics processing units (GPGPU-4). Newport Beach, CA. March
Acknowledgments
This work was supported by the National Natural Science Foundation of China (No. 61162023 and No. 61163046), Education Department Technology Project of Jiangxi (No. GJJ10195) and National Natural Science Foundation of Jiangxi (No. 20114BAB211023).
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Jiang, S., Wang, Y., Chen, Z. et al. Real-time brain extraction method from cerebral MRI volume based on graphic processing units. Neural Comput & Applic 25, 1145–1151 (2014). https://doi.org/10.1007/s00521-014-1588-y
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DOI: https://doi.org/10.1007/s00521-014-1588-y