Megn 536 computational biomechanics
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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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Megn 536 computational biomechanics

MEGN 536 – Computational Biomechanics

Prof. Anthony J. Petrella

Basics of Medical Imaging

Introduction to Mimics Software


Medical imaging

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


Medical imaging1

Medical Imaging

Ultrasound (~1mm)

Ionizing

Non-ionizing

Non-thermal, low

induction

Broken molecular

bonds, DNA damage

May produce heating,

induce currents


X ray imaging roentgenogram

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


X ray imaging

X-ray Imaging

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


X ray imaging1

X-ray Imaging

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


Ct imaging

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


Ct imaging1

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


Megn 536 computational biomechanics

Inhalation

Exhalation


How a ct image is formed

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


How a ct image is formed1

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


How a ct image is formed2

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


Ct image data

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


Ct numbers

CT Numbers

  • CT numbers are expressed in Hounsfield units (HU) and normalized to the attenuation coefficient of water

(atomic number)


Ct numbers viewing a ct image

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


Mr imaging

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


Mr imaging 30 years later

MR Imaging – 30 Years Later

  • “Interesting images, but will never be as useful as CT” –Neuroradiologist (different), 1982

Contemporary Image

First brain MR image


Notes on ct v mr images

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


3d reconstruction

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


Mimics software

Mimics Software

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


What data format does mimics read

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


What if you don t have dicom data

What If You Don’t Have DICOM Data?

  • You will need to use manual input methods with 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


Data in an image file

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


Data in an image file1

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”


Data in an image file2

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)?


Data in an image file3

Data in an Image File

  • 512 x 512 = 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”

  • Total file size is 527,704  header is 3416 bytes


Starting mimics

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 ask if you want to reboot…click “No” or “Reboot Later”

  • If Mimics doesn’t start then on it’s own, attempt to start it again


Mimics tutorials

Mimics Tutorials

  • Complete Lessons 1 and 2 in Mimics SE Course Book, pages 8-28

  • You will need the Mimics SE Course Data, which is posted on the front page of the class website

  • If you don’t have your Course Book, it is also posted on the class website


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