Image Display and Analysis Protocol

Please Review

This tutorial will attempt to guide you through a specific set of functions within VIDA step by step while by-passing an in depth explanation of the multitude of capabilities for each specific module. If you wish to find a more detailed discussion of any of these modules, please click on the smiling face and "have fun."

Starting VIDA

To start VIDA, type vida_start.

Loading Scan

If the image data is not on your computer, you will need to transfer the data to disk before you can load it into shared memory. For more explicit instructions, please see the Tape Utilities section.

Loading Data into Shared Memory

To use VIDA's Region of Interest program to make measurements, you must first load the image data into shared memory. To maximize the contrast of the structures within the lung, you will want to find and load the grey scale values of the lung. Using the LAF:Sample panel, draw a box in the lung. Using the histogram, determine the minimum and maximum grey scale values of the lung. Next, using the LAF:Properties panel, type in the desired Scale Max value and press return. Then type in the desired Scale Min value and press return. If you want to preview what you are about to load, using the LAF:Preview panel, press the loop button to view the image as it will appear after being loaded. For more explicit information on loading data, please see the Loading Image Data section.

MPEG Movie Instructions for loading.

Making Measurements of Airways Using ROI

Overview of How to make Measurements

 To make measurements, you will be using the Region of Interest (ROI) program. To call up the Region of Interest program:

Visualizing the Airways

Display Colors and Contrast

To enhance your ability to view the bronchiole structures, you may wish to change the display colors. We suggest you select the Grey_Screen from the Color Scales menu. For more explicit instructions, please see the Color Scales section. You may also find changing the Window and Level parameters useful for the visualization of the bronchioles. Note, however, that changing the windowing and leveling will change the apparent size of the airways. It is important to realize that you must rely on the ROI: Graph for measurements (this will be discussed in more detail later).

Magnification

The Magnification menu item under the Properties menu button on the Region Of Interest (ROI) window calls up the ROI:Magnification panel. This panel allows the user to scale and pan images on the ROI panel. The upper half of the window is used to magnify the image. The lower half of the window is used for panning the image. Dragging the slider rectangle to the right will increase the image magnification. Dragging the slider rectangle to the left will decrease the image magnification. The full screen button fits the entire image on the ROI canvas. The two sliders in the bottom half of the screen allow the user to move the image left, right, up, or down. Moving the x slider to the right, moves the image to the left allowing you to see the right side of the image. Moving the x slider to the left, moves the image to the right allowing you to see the left side of the image. Moving the y slider to the right, moves the image upward allowing you to see the bottom of the image. Moving the y slider to the left, moves the image downward allowing you to see the top of the image.

Airway Measurements

Airway Lumen Area

In order to accurately quantitate the luminal area of a CT image of the airway, the edge between the soft tissue and the airway needs to be objectively defined. Therefore, we recommend that you use the adjust function which uses an edge detection algorithm.

  1. The ROI:Region Properties panel is on the screen by default when ROI is started. However, you can also call up this panel by selecting the Regions Properties menu item under the Properties menu button on the Region Of Interest main panel.
  2. Select poly from the Create menu of the ROI:Regions Properties panel and draw three polygons as rough estimates of the margin of the airway lumen. It is suggested that these rough estimates be drawn inside rather than outside the lumen so that when the edge is being adjusted, the first edge that is found is the edge which is desired, not some neighboring structure.
  3. Select all polygons using the ROI:Edit/List Regions panel. The ROI:Edit/List Properties panel is on the screen by default when ROI is started. However, you can also call up this panel by selecting the Edit/List menu item under the Edit menu button on the Region Of Interest main panel.
  4. Select smooth from the Modify menu of the ROI:Regions Properties panel and click the right mouse button anywhere on the ROI canvas to smooth the polygons. Continue to smooth the polygons by clicking on the ROI canvas until the polygons are visually smooth (usually about 4 clicks). The smoothing of the initial drawing is of importance since if the original drawing of the edge is jagged, the rays cast in the next step could yield an erroneous path for brightness evaluation.
  5. Select adjust from the Modify menu of the ROI:Regions Properties panel and click the right mouse button anywhere on the ROI canvas to adjust the polygons. The adjust function casts a ray perpendicular to the local contour with half its length inside of the polygon and half outside. The algorithm automatically finds the baseline density of air inside of the airway and the plateau density of soft tissue clearly outside of the airway lumen and the spatial location of the brightness half way between the base and the plateau is defined as the true airway edge; the point on the polygon is moved to this new location. We recommend changing the search length of the adjust function depending on the size of the airway you are currently tracing.
  6. When adjust is selected in the Modify menu, the Edit Region Properties button on the ROI:Region Properties panel calls up the ROI: Adjust Edit Regions Properties panel. This panel can be used to change the distance of the adjust function's search width. We recommend using a length of 6 pixels for airways 4mm diameter or smaller and a length of 16 for larger airways.
  7. After you have adjusted the polygon you will need to smooth it again using smooth from the Modify menu on the Region Properties panel.
  8. You may need to adjust and smooth the polygons several times to get a consistent representation of the airway lumen.
  9. Select all three polygons using the ROI:Edit/List Regions panel.
  10. On the Statistics panel select the Stats for: poly button and select area from the Statistics menu .
  11. Check to see if the units are in pixels or millimeters.
  12. If necessary, press the Properties button on the Stats panel which will call up the Stats:Properties panel, and press the units button to change the units from pixels to millimeters and press the apply button.
  13. Last press the Get Stats button on the Stats panel.
  14. The measurements of each polygon area will appear in the ROI:Stats text editor screen of the Stats panel. We recommend that you use the average of the three polygon areas for the area of the bronchiole lumen.

Airway Wall Thickness

To get measurements perpendicular to the wall, we recommend first finding the center of the airway.
  1. To find the center of an airway for which you have drawn the polygon, select centroid from the Modify menu on the ROI:Region Properties panel.
  2. Select Line from the Create menu on the ROI:Region Properties panel and draw a line through the center of the airway, bisecting the airway wall in an area free of blood vessels.

  3. From the ROI:Stats window select the Stats for: curve button.
  4. From the ROI:Stats window select linear distance from the statistics menu
  5. Select intensity cross from the graph types menu. This will allow you to view the intensity at every point along the selected line.
  6. Measure Line
    Select measure line from the measure menu. This allows you to display the length between two points on the selected curves in the current image on the ROI:Stats text editor. After you select measure line, two vertical lines should appear at either end of the graph.
  7. Move one of the lines to the half-max point of the outer edge of the bronchiole wall. White cross hatches appear along the selected curves to indicate where the vertical lines correspond to on the line.
  8. Move the other line to the half-max point of the inner edge of the bronchiole wall. Example Wall 1, Example Wall 2, Example Wall 3, Example Wall 4.
  9. Left-click on the measure button. The bronchiole wall distance will be displayed in the ROI:Stats text editor. Note: the linear distance statistic must be chosen to display distances in the text editor. Distances are not automatically displayed.
We recommend making at least four wall thickness measurements for each bronchiole, and averaging the measurements.

Saving

Saving the ROIs

Read/Write Button
To save the objects you have drawn to a file or to reload a previously saved file left-click on the Read/Write button on the ROI:Edit/list Region panel. The Read/Write button calls up the Regions to Files panel. Here it is possible to create a file containing all of the objects corresponding to a particular data file. This is valuable because you may want to analyze the file at several different sessions using ROI. Once a region file is created it can be loaded back on to the image data file for additional analysis.

To save a file of objects, choose the appropriate directory and file names on the objects to files window and left-click on the Save file button. To load a file of objects, choose the appropriate directory and file names and left-click on the Load file button. For more explicit instructions, please see the Regions to Files section.

Saving the Statistics File

File Menu Button
The File menu button allows you to save the statistics file. To save the file, select the Save menu item. The Save menu item calls up the Text:Save panel which allows the user to save the text file. Type a filename on the Save entry line, and press the Save button at the bottom right corner of the panel. If no changes have been made since the last save, ROI will inform the user. For more explicit instructions, please see the ROI:Stats section.

VIDA Tutorial Sections Relevant to the Airway Measurement Application Tutorial

 You may find it helpful to review the relevant VIDA tutorial sections.
Tape Utilities
Make Analyze Header
Loading Image Data
LAF:Sample
LAF:Properties
LAF:Preview
Color Scales
Region Of Interest (ROI)
ROI: Region Properties
ROI: Magnification
ROI: Edit/List Regions
ROI: Stats
ROI: Graph




©1994-99 Division of Physiologic Imaging, Dept. of Radiology, Univ. of Iowa


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Last modified: Fri Jun 4 13:55:57 CDT