Image Display and Analysis Protocol

Reviewing Relevant Materials

Starting VIDA

Loading Images

Segmentation

Convert ROI to Image File

Surface Rendering

Visualizing 3-D Movie

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 loaded 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.

Adjusting Contrast

To clarify those hip bones without sacrifice too much detail, you must adjust the contract to make bones stand out and minimize the interference of unnecessary surrounding tissue. Using the LAF:Sample panel, draw a box in the picture containing bones and surrounding tissues. Using the histogram, determine the minimum and maximum grey scale values. Next, using the LAF:Properties panel, type in the desired Scale Max value and press return. The desired maximum should be the LAF:Sample maximum(i.e. 683) + (100 to 150). Then type in the desired Scale Min value and press return. The desired maximum should be the LAF:Sample minimum (i.e. -169) - (100 to 150).

Setting the LAF:Properties panel

If your data set is 16 bit convert it to 8 bit by clicking on the 16 to 8 bit check box
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 Hip Bones

Display Colors and Contrast

To enhance your ability to view the bones, 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.

Segmentation of the Pelvis, Femurs, and Sacrum with Region of Interest (ROI)

ROI is a powerful module to use when irregulated objects need to be segmented. We can name objects with different names to distinguish from each other. This is very helpful for the next step of ROI2IMG convertion.

To call up Region of Interest module:

Pressand hold the right-mouse key 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

Tracing different bones with ROI:

Select the file you want to work on from the ROI:Select Volume/Sequence panel
Choose desired region to create from ROI:Region Properties panel under the Edit menu
Modify regions by selecting options in the Modify panel in the ROI:Region Properties
Name the different bones by changing label in ROI:Edit/List Regions panel
Save ROI file by click the read/write button on the bottom of the ROI:Edit/List Regions panel

Converting ROI File to Image File

After ROI, we have to convert the ROI file to Image file. A program "ROI2IMG/IMG2ROI" is designed for this purpose.

Type in the dimentions of x, y, and z of the image
Define different pixel values for different objects. For example, femur=255, sacrum=253, etc. It is important that these values should be at least 2 pixels apart
Start the Convertion
ROI2IMG/IMG2ROI can not make an appropriate header file for the new image file. Therefore, you must use Make Analyse Header in VIDA to make a new header file

Making a Movie of the 3-D Imgae of the Bones with Surface Render

To call up the Surface Render module:

Press the right-mouse key down on the visualization button on the VIDA main panel
Drag the cursor down to the Surface Render menu item
Release the right-mouse key to select the Surface Render menu item

Rendering 3-D images with Surface Render:

Press the right-mouse key down on the File menu button on the Surface Render panel
Drag the cursor down to the Select Volume/Extract Edges menu item
Release the right-mouse key to select the Select Volume/Extract Edges menu item
The Surface Render:Extract edges panel should appear
Click on Select Volume button and bring up Surface Render:Select Volume panel
Select the image file you want to reconstruct 3-D images from either disk or share memory
Using the min and max sliders, determine the range of pixels you want to extract
The area being extracted will show on the right small canvas in different color
Choosing Smoothing Factor 2 or 3, and Extraction Option as Interpolate
Press the Extract Edges button
When the extraction is finished, select Save Edges from the File menu on the Surface Render panel. Type in the names of Directory and Edge file on the Surface Render:Save Edges panel, and click the Save button
Click the Render button on the top of the Surface Render panel, and the 3-D image will appear on the main canvas
The orientation and rotation of the rendered images can be controlled by choosing Render Parameters from the Edit menu, and the showing objects, colors, and their relative positions on the canvas can be adjusted by choosing Edges Selection

Make a 3-D Movie:

Select Movie Makder from menu
Click Movie Script button from the Surface Render:Movie Maker panel
You can define various things, such as the number of frames, rotation angles, scaling, etc., for your movie in the Movie Script
Save the movie script by click Save Script under the File button
In the Surface Render:Movie Maker panel, choose destination of the movie file, start frame number, end frame number, increment number, and output dimension
Click the Generate button to make a movie

Visualizing 3-D Movie:

Load the movie file from the Load Image Data
Call up the Movie Viewer from the Visualizing Images menu on the VIDA main panel
Select the movie from the Movie: Load Images panel under the File menu
The movie will show on a canvas called Quick Viewer