Analyzing Images
In this chapter . . .
 Calculating statistics for contoured VOIs
 Calculating statistics on VOI groups
 Calculating the volume of masks
 Generating graphs
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.
Rightclick 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.
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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.


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

TBD.
 
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.
 
Opacity

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 voxelsIndicates the number of voxels, including voxels that span frames in an image stack, that are enclosed in the VOI.
 

VolumeMeasures 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. AreaMeasures 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 intensityCalculates 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 intensityCalculates the standard deviation of the intensity of the voxels in the VOI. Center of massIndicates 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.
 
Clear 
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.
 
Range

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 (032K)

Indicates the watershed seed value.
 
Apply

Applies the changes you made to this dialog box.
 
Cancel

Disregards any changes you made in this dialog box and closes the dialog box.
 
Calculate

Runs all selected statistics according to the specifications in this dialog box.
 
Help

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).