matlab-based semi automated method for determining animal bone density from ct images
Post on 13-Jul-2015
694 Views
Preview:
TRANSCRIPT
MATLAB-based Semi-Automated Method for Determining Animal Bone Density
from Computed Tomography (CT) Images
Michael C. OliveiraDepartment of Bioengineering, University of California Riverside
BPBE 510 – Introduction to Medical ImagingFeb 24, 2011
Presentation at a Glance
• Why do we care about bone density?
• What is Computed Tomography?
• Image Acquisition and Experimental Setup
• MATLAB-based Method for Measurements
• CT Images + Density Measurements of Cow, Pig, Fish and Chicken
• Conclusions and Potential Improvements
Why do we care about Bone Density?
• Osteoporosis: the thinning of bone tissue and loss of bone density over time– Bone density measurements can help diagnose or
determine if you are at risk for Osteoporosis– No symptoms in the early stages of the disease
• Tough to catch and diagnose early for preventative treatments
– Late stage symptoms:
– 1 in 5 women over the age of 50 have the disease
• Currently, Dual Energy X-Ray Absorptiometry (DEXA) is the most widely used clinical test for measuring bone density
Info from NIH: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001400
• Bone pain• Fracture without injury• Loss of height
• Lower back pain – spinal fractures• Neck pain – spinal fractures• Stooped posture
Computed Tomography (CT)
Image from: Obenaus lecture 1/12/11, BPBE 510, ‘Computed Tomography’, Slide 5
Computed Tomography (CT)
• Source: Hard X-Rays• Detectors: Scintillators• Image Reconstruction Algorithms:
– Simple Back-Projection– Filtered Back-Projection– And more…!
• Hounsfield Units (HU): normalized value of the X-Ray Attenuation Coefficient. – Air = -1000– Water = 0– Bone can be up to +3000
• Attenuation Coefficient (μ): quantity that characterizes how a material affects EM radiation (units length-1)
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)
Image Acquisition and Experimental Setup
• Four animal bones from Ralph’s– Cow ribs– Pork ribs– Fish skeleton– Chicken leg
• Image Acquisition:– X-Ray Source: 75 kVp– Tube Current: 1 mA– Exposure Time: 175 ms
• Scan time: ~10 mins/data set
• Data sets:– N = 512 images
– Matrix size: 512 x 512
– Intensity encoded using unsigned 16-bit integers [0-(216-1)]
• Images used in analysis:– Cow: 340 – 365
– Pig: 157 – 182
– Fish: 127 – 141
– Chicken: 360 – 385
MATLAB-based Analysis
Read Images into MATLAB
Select Images for ROI selection
Manually select ROIs from Images
ROI mask applied to original images
Average of all densities for all pixels in ROIs
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
• 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
pixel
bonecortmass .,
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
340 349 357 365
157 166 175 182
Co
w R
ibs
Pork
Rib
s
Imaging Geometry
Front View
Top ViewBlack bars represent bones/object
127 133 137 141
360 368 376 385
Fish
Ch
icke
n
Imaging Geometry
Front View
Top ViewBlack bars represent bones/object
Density Measurements
0
0.5
1
1.5
2
2.5
3
3.5
Bo
ne
De
nsi
ty (
g/c
m3)
Animals
Animal Bone Densities
Cow
Pig
Fish
Chicken
Animal Ref Mean BD*
Calc Mean BD*
1Cow 2.1-2.2 2.547 +/- 0.4844
1Pig 2.0-2.1 1.910 +/- 0.4729
Fish ND 2.526 +/- 0.3747
1Chicken 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)
Conclusions
• Successfully scanned and acquired images
• Wrote a semi-automated software package in MATLAB for determining bone density
• Results from the software are fairly accurate compared to literature values
Potential Improvements
• Image acquisition geometry– Set up specimen to avoid the rings or artifact
• OR find robust way to filter out artifacts
– Contributes to improving automation
• Improve the repeatability and throughput– Improve the automation
• Move towards fully automated processing instead of manual ROI selection
– Improve processing speed• Offload some computation to Graphics Processing Units (GPUs)
using Jacket to decrease total processing time
• Use an object with known attributes (density) for calibration– Should increase accuracy when converting pixel intensity
to HU
Acknowledgments
• Biophysics and Bioengineering, Loma Linda Univ.
– Non-Invasive Imaging Lab
• Bioengineering, UC Riverside
• Funding Source
– Personal CHASE Acct. Num: #XXXXXXXXX
Convert kVp to X-Ray Energy
• Conversation of Energy
• Potential Energy = Kinetic Energy = X-Ray Energy
• EX-Ray = 74.9 keV
• λ = 1.65 x 10-11 m (Hard X-Rays)
hcmveV
EKEU RayX
2
2
1
V = 75 kVp (75,000V)e = elementary charge = 1.602 x 10-19 Cm = 9.109 x 10-31 kgh = Planck’s constant = 4.135 x 10-15 eV sc = Speed of light = 3 x 108 m/s
Linear Interpolation of Mass Attenuation Coefficients
inputPt - lowerBound
upperBound - lowerBound=
InterpValue- lowerBoundVal
upperBoundVal - lowerBoundVal
0.00
0.20
0.40
0.60
0.80
1.00
1.20
1.40
0.00 20.00 40.00 60.00 80.00 100.00
Mas
s A
tte
nu
atio
n C
oe
ffic
ien
t (c
m2 /
g)
X-Ray Energy (keV)
Mass Attenuation Coefficient vs. X-Ray Energy
Cortical Bone
Water
μwater= 0.1893 cm2/g μmass,cort.bone= 0.2526 cm2/g
Reproduced from data at 2 NIST Physical Measurements Laboratory, http://physics.nist.gov/PhysRefData/XrayMassCoef/tab4.html
top related