Liver Volume VIDA Tutorial

Region of Interest Volume Measurements

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."

Start VIDA

Type vida_start.

Loading Images

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 Images into Shared Memory

To use VIDA's Volume Render Program, you must first load the image data into shared memory.

Maximizing Contrast

To maximize the contrast of the structures within the liver, you will want to find and load the grey scale values of the liver and its immediate surrounding tissue. Using the LAF:Sample panel, draw a box in the liver. Using the histogram, determine the minimum and maximum grey scale values.

For example, using the histogram the following values were obtained:

min = -105

max = 160

The desired Scale Min and Max can be obtained from the following formulas:

Scale Min = histogram min - (100 to 150)

Scale Max = histogram max + (100 to 150)

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.

Setting the LAF:Properties panel

Make sure you entered the proper Scale Max and Scale Min values -- review how to

Previewing What you are about to Load

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.

Visualizing the Liver

Display Colors and Contrast

To enhance your ability to view the liver, you may wish to change the display colors. We suggest you select heat or 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 visualization.

Region of Interest

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

To call up the Region of Interest module:

Press the right-mouse key down on the Analysis button on the VIDA main panel
Drag the cursor down to the Region of Interest menu item
Release the right-mouse key to select the Region of Interest menu item

Example Liver ROI Tracings

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.

Liver Volume Measurements

In order to accurately and consistently define the liver area of a CT image. The edge between the soft tissue and the surrounding tissues needs to be objectively defined. Therefore, we recommend that you use the adjust function which uses an edge detection algorithm.

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.
Select poly from the Create menu of the ROI:Regions Properties panel and trace the edge of the liver. It is better to draw slightly on the inside rather than the outside of the liver so that when the edge is being adjusted, the first edge that is found is the edge of the liver not the edge of the another structure like the abdominal wall, for instance.
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 liver trace by clicking on the ROI canvas until the polygon is 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.
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 tissue inside of the liver and the plateau density of tissue outside of the liver and the spatial location of the brightness half way between the base and the plateau is defined as the true liver edge; the point on the polygon is moved to this new location.
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 to 8 pixels for the liver.
After you have adjusted the polygon you will need to smooth it again using smooth from the Modify menu on the Region Properties panel.
You may need to adjust and smooth the polygon several times to get a consistent representation of the liver.
You may also want to edit (redraw) a section of the liver trace. To do this, Select edit from the Modify menu of the ROI:Regions Properties panel and use your mouse to redraw the trace.
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.
Right-click on the Select button
Drag your cursor down to the select all menu item
Release the right mouse button to select the select all menu item
On the Statistics panel select the Stats for: poly button and select volume from the Statistics menu.
Check to see if the units are in pixels or millimeters.
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
If necessary, enter the correct slice thickness on the Z entry line. Slice thickness must be the distance from the center of one slice to the center of the next slice.
Left-click on the apply button.
Left-click on the Get Stats button on the Stats panel.
A warning message will appear
The measurements of the liver volume will appear in the ROI:Stats text editor screen of the Stats panel.

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.