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MEGN 536 – Computational Biomechanics

MEGN 536 – Computational Biomechanics. Prof. Anthony J. Petrella Basics of Medical Imaging Introduction to Mimics Software. Medical Imaging. Used for measuring anatomical structures… size, shape, relative position in body Can reconstruct geometry for modeling purposes X-ray techniques

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MEGN 536 – Computational Biomechanics

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  1. MEGN 536 – Computational Biomechanics Prof. Anthony J. Petrella Basics of Medical Imaging Introduction to Mimics Software

  2. Medical Imaging • Used for measuring anatomical structures… size, shape, relative position in body • Can reconstruct geometry for modeling purposes • X-ray techniques • planar x-rays, mammography, chest x-ray, bone fracture • CT scans – computed tomography • Nuclear imaging, radioactive isotope • planar imaging, bone scan • positron emission tomography (PET) • MRI – magnetic resonance imaging • Ultrasound

  3. Medical Imaging Ultrasound Ionizing Non-ionizing Non-thermal, low induction Broken molecular bonds, DNA damage May produce heating, induce currents

  4. X-ray Imaging (Roentgenogram) • Wilhelm Röntgen (1845-1923) • Nov 1895, announces X-ray discovery • Jan 1896, images needle in patient’s hand • 1901, receives first Nobel Prize in Physics Röntgen’s wife, 1895

  5. X-ray Imaging • X-ray film shows intensity as a negative ( dark areas, high x-ray detection)

  6. X-ray Imaging • X-ray film shows intensity as a negative ( dark areas, high x-ray detection) = radiolucency

  7. CT Imaging • Computed tomography • Tomography – imaging by sections or sectioning, creation of a 2D image by taking a slice through a 3D object • 2D images are captured with X-ray techniques • X-ray source is rotated through 360° and images are taken at regular intervals • CT image is computed from X-ray data

  8. CT Imaging • Developed by Sir Godfrey Hounsfield, engineer for EMI PLC 1972 • Nobel Prize 1979 (with Alan Cormack) • “Pretty pictures, but they will never replace radiographs” –Neuroradiologist 1972 early today

  9. Inhalation Exhalation

  10. How a CT Image is Formed • X-ray source is rotated around body for each slice • Patient is moved relative to the beam • Figure below does not show it well, but the X-ray beam has a thickness  each slice has a thickness Note: slice thickness http://www.sprawls.org/resources/CTIMG/module.htm

  11. How a CT Image is Formed • Figures below show only two views 90° apart • A process of “back projection” is used to indicate regions where X-ray attenuation is greater – i.e., tissue is more dense

  12. How a CT Image is Formed • Example at left w/ only 2 views shows poor image • Clinical CT uses several hundred views for each slice • Data collected in matrix

  13. CT Image Data • Recall that each CT slice has a thickness  each element in the data matrix for a single CT slice represents a measurement of X-ray attenuation for a small volume or “voxel” of tissue • X-ray attenuation is expressed in terms of the X-ray attenuation coefficient, which is dependent primarily on tissue density

  14. CT Numbers • CT numbers are expressed in Hounsfield units (HU) and normalized to the attenuation coefficient of water (atomic number)

  15. CT Numbers & Viewing a CT Image • CT numbers usually recorded as 12-bit binary number, so they have 212 = 4096 possible values • Values arranged on a scale from -1024 HU to +3071 HU • Scale is callibrated so air gives a value of -1024 HU and water has a CT number of 0 HU • Dense cortical bone falls in the +1000 to +2000 HU range 0-2000 HU 1000-2000 HU

  16. MR Imaging • Magnetic resonance imaging • 1946: Felix Block and Edward Purcell discover magnetic resonance • 1975-1977: Richard Ernst and Peter Mansfifield develop MR imaging • An object is exposed to a spatially varying magnetic field, causing certain atomic nuclei to spin at their resonant frequencies • An electromagnetic signal is generated and varies with spatial position and tissue type • Hydrogen is commonly measured – hence, good contrast for soft tissues that contain more water than hard tissues like bone

  17. MR Imaging – 30 Years Later • “Interesting images, but will never be as useful as CT” –Neuroradiologist (different), 1982 Contemporary Image First brain MR image

  18. Notes on CT v. MR Images • CT image based on X-ray beam attenuation, depends on tissue density • CT images generally regarded as better for visualization & contrast in bone imaging • Bone density and modulus can be estimated • MR image based on resonance of certain atomic nuclei, e.g. hydrogen • MR images generally regarded as better for visualization & contrast in imaging soft tissues, which contain more water than bone

  19. 3D Reconstruction • CT & MR images represent 2D slices through 3D anatomic structures • 2D slices can be “stacked” and reconstructed to form an estimate of the original 3D structure

  20. Mimics Software • Mimics (www.materialise.com/mimics) is the leading commercial software program for reconstruction of CT & MR image data

  21. What Data Format Does Mimics Read? • Most medical images are saved in the DICOM image format • What is DICOM? • The standard for Digital Imaging and Communications in Medicine • Developed by the National Electrical Manufacturers Association (NEMA) in conjunction with the American College of Radiology (ACR) • Covers most image formats for all of medicine • Specification for messaging and communication between imaging machines • You don’t need to know the details of the format, but Mimics is happiest when reading DICOM images

  22. What If You Don’t Have DICOM Data? • You will need to use manual input methods with Mimics to read the data • You need to know something about the images • A CT or MR scan consists of many slices • We will be focused on bone modeling, so CT data will be our main interest • It is also important to remember how a CT image slice is formed and what data it contains

  23. Data in an Image File • The format of CT numbers in the data file depends on the precision of the binary data • For CT numbers, we only need to cover the 12-bit range,-1024 to 3071 • short has 2 bytes = 2 × 8 bits/byte = 216 binary values = 65,536 • When using unsigned shorts the data is shifted so all CT numbers are positive  0 to 4095

  24. Data in an Image File • Recall a single CT slice is a matrix of data • 512 x 512 is a common size  262,144 pixels • Each element in the matrix represents a pixel value with a binary format of “short”, therefore each pixel contains 2 bytes of data • 262,144 x 2 = 524,288 bytes, any additional data is part of the “header”

  25. Data in an Image File • Visible Human link on class website • Data are available for download • Download sample of Visible Human data from today’s Class Notes page • These images are 512 x 512 and the data format is unsigned short • How large is the header (bytes)?

  26. Starting Mimics • You should find a Mimics icon on the desktop… or • Find “Materialise Software” in Start menu… or • Type “Mimics” in the Start menu search box • Run Mimics • The software should start right away, if not, there may be a licensing error on your computer

  27. Manual Import – Visible Human Data • Import the Visible Human data you downloaded • These data are not DICOM, they are a proprietary GE file format • We do not have a GE import module for these data  you will need to “Force raw import”

  28. Manual Import – Visible Human Data • Make other settings as shown below

  29. Viewing a CT Image • Play with contrast window to change appearance • Window width applies to CT numbers – CT numbers above window appear white, CT numbers below window appear black • Window level applies to gray values – level controls center and range of gray values width level

  30. Pixel Unit • Check the setting that Mimics uses for pixel units • OptionsPreferences… • Change between HounsField and GrayValues and observe the effect it has on the values displayed in the contrast window • Does this make sense?

  31. Mimics Software • You may install Mimics on your personal machine • You must run through VPN in order to get a network license • Installation file and instructions are posted on main page of class website

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