Post on 30-Jul-2015
GPU-accelerated method for determining animal bone density from computed tomography (CT)
images
Michael C. OliveiraDepartment of Bioengineering, University of California Riverside
EE 217 – GPU Architecture and Parallel ProgrammingMar 22, 2013
Computed Tomography (CT)
Image from: Obenaus lecture 1/12/11, BPBE 510, ‘Computed Tomography’, Slide 5
Resulting CT Image
http://www.columbusimaging.com/Brilliance_CT_3.jpg
Typical CT Scanner
Colormap for CT Images:Black: low X-Ray Attenuation, lower signal intensityWhite: high X-Ray Attenuation, higher signal intensity
Signal Intensity ~ Hounsfield Units and
Attenuation Coefficient
http://radiographics.rsna.org/content/22/4/949/F7.medium.gif
Source-Detector Geometry
Image Processing Algorithms (from
Detector data)
Previous Work
0
0.5
1
1.5
2
2.5
3
Animal Bone Densities
Cow
Pig
Fish
Chicken
Animals
Bone
Den
sity
(g/c
m3)
Animal Ref Mean BD*
Calc Mean BD*
1Cow 2.1-2.2 2.547 +/- 0.48441Pig 2.0-2.1 1.910 +/- 0.4729
Fish ND 2.526 +/- 0.37471Chicken 2.1-2.2 2.017 +/- 0.7940
*Density in g cm-3
1 Aerssens et al. “Interspecies Differences in Bone Composition, Density and Quality: Potential Implications for in Vivo Bone Research.” Endocrinology. 139(2): 663-670. (1998)
Hardware/Software SetupLenovo U410 Ultrabook
CPU GPU
Intel Core i5-3317U @ 1.70 GHz NVIDIA GeForce 610M
8.00 GB RAM 1 GB DRAM
Dual-core CPU 1 SM x 48 CUDA cores
Programmed with MATLAB and C++ in Visual Studio 2008
Programmed with CUDA 4.2 in Visual Studio
CT images are 512 x 512 pixels with 16-bit encoding
Hybrid Program Flowchart
Host and Device memory allocations
Read image and image mask data
Copy image and image mask to GPU
Load image and image mask into shared memory
Compute density per pixel and apply mask
Parallel reduction sum per block
Write block sums to global memory
Copy block sums to CPU
Compute average density from block
sums
CPU GPU
ROIs scaled to Hounsfield Units
Hounsfield units converted to Atten.
Coeff.
Atten. Coeff converted to Mass
Atten. Coeff
Density solved for each pixel in ROI
• Scale the Pixel Intensities to the Hounsfield Scale
• Conversion from Hounsfield Units to Attenuation Coefficient
• Solve for Density using the relationship between Attenuation Coefficient and Mass Attenuation Coefficient
)min(max
)min),,((
)min(max
)min(
CTimageCTimage
CTimagezyxCTimage
rscValHUrscValHU
rscValHUrscValHU
water
waterpixelHU
1000
pixel
pixelbonecortmass
.,
ROIs scaled to Hounsfield Units
Hounsfield units converted to Atten. Coeff.
Density solved for each pixel in ROI
Atten. Coeff converted to
Mass Atten. Coeff
2μwater= 0.1893 cm2/g @ 75 keV
2μmass,cort.bone= 0.2526 cm2/g @ 75 keV
CT Scale: [0, 65535]1HU Scale: [-1000, 3000]
1 Bushberg, Jerrold T. "Computed Tomography" The Essential Physics of Medical Imaging. Philadelphia: Lippincott Williams & Wilkins, 2002.2 NIST Physical Measurements Laboratory, http://physics.nist.gov/PhysRefData/XrayMassCoef/ComTab/bone.html
Results
Ref. C++ CUDA
BD* BD* Time (ms) BD* Time (ms) Speedup
1Cow 2.1-2.2 2.6718 5.134 2.6716 2.087 2.460x
*Density in g cm-3
1 Aerssens et al. “Interspecies Differences in Bone Composition, Density and Quality: Potential Implications for in Vivo Bone Research.” Endocrinology. 139(2): 663-670. (1998)
Code Block Time (ms)
CPU --> GPU copy 0.544
CUDA Kernel 0.036
GPU --> CPU copy 1.512
Total 2.097
98% time spent doing data transfer2% time doing computation
Timing done using QueryPerformanceCounter()