Analyzing Images

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In this chapter . . .

You can use MIPAV to generate statistics on contoured volume of interest (VOI) regions and to calculate the volume of painted pixels and voxels. You can also use MIPAV's algorithms to perform more sophisticated image analysis. For information about algorithms, refer to Volume 2, Algorithms.

Calculating statistics for contoured VOIs

Once you have contoured structures, you can generate statistics on the VOI.

To select the type of statistics to calculate for a single VOI
1 Open an image.
2 Contour a VOI. An example of a contoured VOI is shown below (Figure 1).
3 Select the VOI.
4 Do one of the following:
Select VOI > Properties.
Right-click inside the VOI, which automatically selects it. Then select Properties on the menu (Figure 1).
The VOI Statistics dialog box (Figure 2) opens.
5 Choose the types of statistics that you want the program to calculate by selecting the appropriate check boxes in the Statistics to calculate group.
Refer to Figure 2 for information on each statistic you can select.
6 Click Calculate.

Figure 1. VOI properties context menu

ZeroBased VOIProperties.jpg


Figure 2. VOI Statistics dialog box

Name of VOI
Indicates the color of the VOI outlines and the name of the VOI. To use this to group two contours, refer to Chapter 7 for more details.

ZeroBased VOIPropertiesDialogbox.jpg

Show bounding box
Indicates whether to show the bounding box. If this check box is selected, the bounding box appears around the VOI.
Use Additive polarity for VOI
Include for processing
Indicates whether to include the VOI in the processing when running an algorithm. If selected, the VOI is included.
Boundary or blended
Indicates whether the contour is filled with color (blended) or transparent (only the boundary appears). If selected, the VOI is filled with color.
Indicates whether a VOI that is filled with color is transparent, translucent, and opaque: 0 is transparent, and 1 is opaque.
Statistics to calculate
# of voxels-Indicates the number of voxels, including voxels that span frames in an image stack, that are enclosed in the VOI.
Volume-Measures the amount of space occupied by a 3D VOI. To calculate the volume, the software multiplies the number of pixels by the resolution of each dimension.
Area-Measures the surface of the VOI. To calculate the area, the software multiples the number of pixels by the resolutions of the x and y dimensions.
Perimeter - measures a perimeter of VOI.
Min. Intensity - shows the min voxel intestacy.
Max. Intensity - shows the max voxel intensity.
Average voxel intensity-Calculates the average intensity of the voxels in the VOI by adding the intensity of all voxels in the VOI and dividing the result by the sum of the voxels.
Std. dev. of voxel intensity-Calculates the standard deviation of the intensity of the voxels in the VOI.
Center of mass-Indicates the point at which the whole mass of the VOI is concentrated. It is calculated as the sum of all x coordinates divided by the number of points and the sum of all y coordinates divided by the number of points.
Principal axis (only 2D)-Calculates the principal axis for 2D images only.
Eccentricity (only 2D)-Describes the geometric shape of the VOI as an ellipse, with 0 indicating a circle and 1 indicating a straight line.
Major axis length - calculates the length of the major axis for an elliptical VOI.
Minor axis length - calculates the length of the minor axis for an elliptical VOI.

Clears all of the statistical measures in Statistics to calculate.

Select all
Selects all of the statistical measures in Statistics to calculate.
Exclude intensity range
Excludes a specific range of intensity values, which you specify in the Range boxes, in the calculation. When this check box is selected, the Range boxes become available.
Specifies a particular range of intensities to exclude from the calculations. These boxes become available only when the Exclude intensity range check box is selected.
Watershed seed value (0-32K)
Indicates the watershed seed value.
Applies the changes you made to this dialog box.
Disregards any changes you made in this dialog box and closes the dialog box.
Runs all selected statistics according to the specifications in this dialog box.
Displays online help for this dialog box.

To view the statistics for a single VOI
1 Select the Output window.
2 Select the Data tab on the Output window to view the information. The Data page of the Output window (Figure 3) appears showing the results of the calculations.

To save the statistics for a single VOI
1 Select File > Save Messages in the Output window.
The Save dialog box opens.
2 Specify a name for the messages file and select a location for storing it.
3 Click Save. The software saves the file and places it in the specified location.
Tip: MIPAV provides you with the ability to type directly onto the Data page. So, for example, you could add a description of when the statistics were calculated or any other such meaningful information (Figure 3).

Figure 3. Data page in the Output window showing statistics


Calculating statistics on VOI groups