An Activity in Computed Tomography

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1 Pre-lab Discussion An Activity in Computed Tomography X-rays X-rays are high energy electromagnetic radiation with wavelengths smaller than those in the visible spectrum ( nm and nm respectively). As X-rays pass through a person some of the X-rays will be absorbed, meaning fewer X- rays leave the body than entered it. This is called attenuation and is larger (fewer exiting X-rays) for denser material. Bone, for example, attenuates X-rays more than muscle since bone is denser. Images produced with X-rays are like shadows, showing where the X-ray radiation passed through the body and where it was absorbed. Dark regions on an X-ray image correspond to tissue with smaller attenuation coefficients and lighter regions with denser tissue like bone (see Fig. 1.1). The main drawback to X-ray imaging is that intense or prolonged exposure leads to serious health problems such as cancer and radiation burns. High energy X-rays can change the molecular structure of tissue, sometimes causing a person s DNA to mutate faster than normal. Because of this drawback, the goal of all forms of X- ray imaging is to acquire the best possible image while submitting the patient to the lowest possible dose of radiation. Computed Tomography One of the limitations of planar images like chest X-rays are that they are a two dimensional representation of a three dimensional object. This limits the amount of information that can be discerned. For example, an X-ray of a box, in which a cone and sphere are placed, may look something like Fig. 1.2 (a). From this we may be able to say what kind of objects they are but not their relative locations. For example, is the sphere in front of the cone or is the cone in front of the sphere? But if we rotate the X-ray 90 o relative to the box we may get an image like Fig. 1.2 (b). This is the basic idea behind Computed Tomography where multiple X-rays scans from different angles are put together to form an image. Of course this also means that the radiation dose for a CT scan is larger than for a regular single X-ray scan. (a) (b) Fig. 1.1 Cranial CT scan. The white region is the skull and the darker regions are soft tissue. Source: Computed Tomography: From Photon Statistics to Modern Cone-Beam CT Fig. 1.2 Projections of a sphere and a cone. (a) a single image imparts a limited amount of information (b) another image at a different angle can reveal additional information Instructor Note: Question for students: How does an X-ray film look before it is used? Answer: It s all white! Just like the parts that included bone during an exposure. Exposure to X- rays will darken the film. The cone/sphere example could be done as a demonstration during the lecture. Place some kind of screen in front of the objects so the students can t see their positions. Then place a light source in front of the objects to produce Fig. 1.2(a). Ask the students what they can say about the objects. Then ask if there is any way to find out which object is in front. X-ray/CT Topics Covered X-rays are 2D representations of 3D area CT reveals information a single X-ray does not Exposure to X-rays can be dangerous

2 Back Projection Back projection is one of the most common methods for reconstructing an image. The images in Fig. 1.2 are called projections. In a CT scanner, an X-ray source rotates around an object producing area projection data at each angle. That data is spread back onto an image of the area, which is divided into pixels. Pixels are the individual units of the reconstruction. Each pixel has a certain value attached to it which corresponds to the attenuation at that point (Fig. 1.3). When put together, all the pixels reveal an image. As more and more X-ray scans are taken and data is back projected, an image of the area starts to emerge similar to what is shown in Fig It is important to note that because projection data are collected from multiple angles, CT imaging results in a higher dose of radiation than planar imaging. Today patients receiving a CT scan are exposed to the equivalent of 30 to 442 chest x-rays per scan The near IR-light used in a photogate has a larger wavelength (880nm) and lower energy than X- rays. Infrared light is quickly attenuated by water inside the human body and is not suitable for medical imaging of deep tissue. However, it is able to pass through material with low attenuation coefficients like the light filter used in this experiment. The projection data recorded by the photogate will be a digital signal of 0 (unblocked) and 1(blocked), rather than the continuous signal of an X-ray based CT scanner (Fig. 1.3). Photogate scans Back Projection Photogate scans Fig. 1.3 Projection data is smeared back onto a reconstruction of the scanned area. Pixels of higher values correspond to the position of the object. The projection data are the 0s and 1s to the right and bottom of the first grid and represent the unblocked and blocked states of the photogate respectively. Instructor Note: As a demonstration of back projection shine two light sources on a cylinder at a right angle. Explain that just as the two shadows converge at the cylinder s position, back projection data converge at the location of scanned objects. This also emphasizes the correlation between X-rays and shadows. Back Projection Topics Covered Projections Back Projection is spreading the projection onto the grid Back projection grid divided into pixels High values in the reconstruction correspond to the position of the object 2

3 Geometry Once the Photogate is blocked and we have projection data to work with, the computer spreads that data back onto the reconstruction graph. To do this we need to mathematically describe each scan. This requires us to find an equation for the imaginary line from the light source of the photogate to the detector, relative to the scanned area. The only data we have as inputs are (1) the distance between the rotational axis and the origin Focus-Center-Distance (FCD) (see Fig. 2.2), (2) the angle between the rotational axis and the negative x-axis,θ, and (3) the angle between the FCD and the scanning line,φ, (Fig. 1.4). Rotational Axis y φ IR Source Scanning line Focus-Center-Distance (FCD) IR Detector θ x Fig. 1.4 Geometry of the CT scanner, the Scanning line represents the line connecting the light source and detector of the photogate We can use geometry and trigonometry to find the equation of the scanning line. All we need are some trig identities (SOH CAH TOA) and the formula for a line (y=mx+b). There are multiple formulas we use to describe specific scanner geometries. Which formula we choose for the scanning line changes depending on the values ofθ, φ and the FCD. Each possibility is programmed into LabVIEW, which selects the appropriate formula based on the inputs. 3

4 Computed Tomography Experiment Guide Introduction In this activity students will be given a mystery box, in which 1 to 3 cylinders were placed by the instructor before class. This enclosure should be sealed so that students don t know the locations of the cylinders. The students will use a photogate, rotary motion sensor and a LabVIEW program to make an image of the contents of the enclosure. Using that image, they will determine the position and dimensions of the cylinders inside. Objectives After completing this lab, students should be able to: Describe the basics of how Computed Tomography makes an image through back projection. Demonstrate a practical application of SOH CAH TOA and the line equation y=mx+b. Understand terms important to CT such as image artifacts and windowing Find the location and diameters of objects inside an opaque mystery box Equipment Vernier photogate (with rod), rotary motion sensor (with pulley) and LabPro Clamp to attach the photogate to the rotary sensor Rotating platform and base with angular scale Angular indicator Rotary sensor stand Congo Blue #181 light filter enclosure Cylinders of various diameters (~0.5 2 cm) Fig 2.1 Apparatus setup 4

5 LabPro/Computer Setup 1) Make sure the LabPro is connected to a USB port 2) Plug the photogate into the Dig/Sonic 1 jack and the rotary motion sensor into the Dig/Sonic 2 jack. Apparatus Setup 1) Assemble the apparatus as shown in Fig Make sure that the rotation sensor stand and the rotation table stand are aligned and that the angular indicator points straight down the x-axis. 2) Lower the rotary sensor so that the degree indicator is just resting on the rotating platform. This will help stabilize platform. (Using a heavy rotary sensor stand reduces the chances of moving the rotary sensor during the experiment.) 3) Adjust the apparatus as needed so the photogate is free to pass over the mystery box. 4) Measure the Focus-Center-Distance (the distance in cm between the shaft of the rotation sensor to the center of the platform). Record it in the space below. FCD = (cm) FCD Fig. 2.2 The Focus-Center-Distance (FCD) is the distance between the shaft of the rotary sensor and the center of the rotating platform. 5

6 Apparatus Calibration Open the program Computed Tomography and click on Manual Scanner. Follow the on-screen instructions. It is important that the two stands are aligned and that the angular indicator points straight down the x- axis. If they are not correctly positioned, the resulting image will be distorted. To verify that the apparatus is positioned correctly, perform the following test. 1) Place a cylindrical object at the center of the grid on the platform 2) Enter the FCD you recorded in the Apparatus Setup section. 3) Making sure the photogate is not blocked, click on BEGIN SCAN. Slowly move the photogate over the object placed at the origin. The image in the reconstruction graph should be symmetric about the x-axis (Fig. 2.3). If the image is not symmetric: a. Realign the rotary sensor stand and the rotating platform b. Re-zero the rotating sensor c. Repeat this procedure until the image is symmetric While performing this test, take note of the scanning speed needed to produce a good image. Does a slower or faster scan rate produce better data? (a) Bad Calibration (b) Good Calibration Fig Two scans of the same cylinder positioned at the origin. (a) The image is not symmetric about the x-axis. Make sure the rotating platform base and the base holding the rotary sensor are aligned and re-zero the rotary sensor. (b) The two bases are properly aligned and the rotary sensor was correctly zeroed; therefore the scan of the cylinder is symmetric about the x-axis. 6

7 Data Collection Using a Cylinder at the Origin 1) With the cylinder still at the origin, do multiple scans at differing speeds. Which speed do you think will result in a higher quality scan? There is a certain amount of computer processing time needed to read the data and spread its back projection onto the graph. Moving the photogate too quickly can result in image artifacts. Could slower scan times be dangerous in medical CT? Why? Slower scan times would mean longer exposure to radiation, which means a greater possibility of injury. 2) Change the pixel count by incrementing the Pixel/cm control and clicking SET PIXEL COUNT and scan the cylinder (increment Pixel/cm by at least 10 initially). How do image quality and scan time change with an increased pixel count? Why? An increased pixel count generally results in a higher quality image, but a longer scan time, because more computations are required to create an image. The increased scan time could also result in more image artifacts.lowering the pixel count is the simplest way to handle computers with slower processors or data acquisition units. Using the Mystery Box 1) Place the enclosure on the grid, align the photogate with the x-axis and rotate the platform 360 o to make sure that the enclosure and the photogate won t touch during the scan. In order to ensure the grid inside the enclosure and the grid on the platform align, the instructor may wish to draw marks on the enclosure at the axes. The students can then align the marks with the axes on the platform. 2) With the photogate at the starting position, click BEGIN SCAN. Slowly move the photogate over the enclosure. A single pass should take 15 to 20 seconds. 3) Once the photogate has made a complete pass, rotate the platform, enter the new θ and scan the enclosure again. Repeat for desired number of θ angles. For your first scan try scanning in 20 o increments. An image artifact is a false representation of the actual scanned area. Does your final image show any artifacts? What caused the artifacts? In addition to the actual objects, the reconstructed image shows extra data that resulted from back projecting data. Artifacts may have also been caused by improper scanning techniques. 7

8 4) Adjust the Window slider to highlight important data. Describe why the image is changing. The Window slider sets the low value of the color table. Pixels with values smaller than that of the slider will be black, because black is the lower boundary on the color table. Describe how changing the Window improved the image. Changing the Window slider removes some of the artifacts caused by the reconstruction algorithm. In medical CT scanners, windowing can also be used to improve the contrast between similar media. 5) Right click on the cursor toolbar and click on Create Cursor>Free. Using the cursor(s) determine the position and diameter of each object. To display a cursor, right click on the cursor area below the graph and go to Create Cursor>Free. Click and drag the intersection of the two lines of the cursor to the center of the object. The corresponding grid markers on the left and bottom of the scan area indicate the location. Do the objects in your scan look circular? If not, what could be done to improve your image? Possible methods to improve image quality: Decrease the increment between θ (every 10 o instead of every 20 o ) Increase the pixel count Scan the enclosure more slowly 8