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)

Question:How can we use Computed Tomography (CT) to

measure bone density?

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

Program Interface

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

Questions??

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