Creating a mask using the Paint Grow Segmentation method and Generating graphs: Difference between pages

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You can create a mask using the paint grow segmentation method, which uses voxel aggregation to group voxels into larger regions. You begin by selecting a voxel to serve as the ''seed point,'' or starting point. The software applies paint color to all voxels touching the seed point that fall within the intensity range that you specify.<br />'''Note:''' You cannot apply the paint grow segmentation method to RGB images.<br />
MIPAV allows you to generate intensity profiles, or contour VOI graphs, for VOI contours. For delineated VOIs, you can generate 2D, 3D, or 4D intensity graphs. You can also generate a 3D intensity graph at a specific point across all slices in a dataset. For information on how to contour a VOI, refer to Chapter 1, "Segmenting Images Using Contours and Masks,"<br />


==== To create a mask using the Paint Grow tool ====
=== Generating contour VOI graphs ===
[[Image:FillsAreaIco.jpg]] - Fill an Area with Desired Color<br />
Contour VOI graphs display the intensity values of the selected contour's boundary in the Contour VOI Graph window (Figure 10). You can generate either 2D or 3D contour VOI graphs. <br />
1 Click the Fill an Area with Desired Color icon. The Paint Grow dialog box appears (Figure 9).<br />
2 Select the seed point, which is used as a starting point for the paint grow operation. To do this, move the pointer to the image. As you move the cursor, the location and intensity of the voxel under the pointer tip appears in the Cursor position and voxel intensity text box. Click the voxel you want to designate as the seed point.<br />
3 Adjust the delta values and parameters. <br />
4 Click Apply when complete to begin the paint grow method. The Paint Grow dialog box closes.<br />''' To correct the mask<br /></font>'''</div>


If the results are not what you want, do the following:
'''To generate 2D contour VOI graphs'''<br />
1 Open an image.<br />
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br />


1 Click the Paint Grow button. The Paint Grow dialog box appears.<br />
2 Select the seed point, which is used as a starting point for the paint grow operation. To do this, move the pointer to the image. As you move the cursor, the location and intensity of the voxel under the pointer tip appears in the Cursor position and voxel intensity text box. Click the voxel you want to designate as the seed point.<br />
3 Adjust the delta values and parameters. <br />
4 Click Apply when complete to begin the paint grow method. The Paint Grow dialog box closes.<br />
If the results are not what you want, do either of the following:<br />
Click the Undo last region paint icon, and start again.<br />
Click the Erase icon, or click, the Erase all paint icon, to erase all paint.<br />


'''To commit the mask'''<br />
{| border="1" cellpadding="5"
|+ '''Figure 10. Contour VOI Graph window '''
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[[Image:windowContourVOIGraph.jpg]]
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open Graph</font>'''</span>-Opens a PLT file that contains graph data. When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears. </div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Save Graph</font>'''</span>-Saves the graph data in a PLT file. When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Print Graph</font>'''</span>-Allows you to print the graph. When you select this command or press <br />Ctrl P, the Print dialog box opens.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Close Graph</font>'''</span>-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</font>'''</span></div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Delete Function</font>'''</span>-Allows you to delete a specific function. However, you cannot delete a function if it is the only function displayed in the window.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Copy Function</font>'''</span>-Copies a function that is currently displayed in the window.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Paste Function</font>'''</span>-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Views</font>'''</span></div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Modify Graph Features</font>'''</span>-Allows you to customize the appearance of the graph.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Range to Default</font>'''</span>-<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[TBD]</font>'''</span></div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Graph to Original</font>'''</span>-<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[TBD]</font>'''</span>. </div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help Topics</font>'''</span>-Displays online help topics.</div>
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Click one of the following commit buttons:
<br />
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
*Select VOI &gt; Graph &gt; Boundary Intensity in the MIPAV window. <br />
*Right click on the VOI and then select Graph &gt; Boundary Intensity.<br />
*The Contour VOI Graph window (Figure 10) opens.<br />


[[Image:MasksInsidePaintedAreaIco.jpg]] - the Masks Inside Painted Area icon.<br />[[Image:MasksOutsidePaintedAreaIco.jpg]] - the Masks Outside Painted Area icon.<br />
'''To generate 3D contour VOI graphs'''<br />
1 Open an image.<br />
2 Delineate a VOI on the image using the 3D rectangular VOI icon, in the MIPAV window. <br />
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
*Select VOI &gt; Graph &gt; Boundary Intensity in the MIPAV window.<br />
*Right-click on the VOI and then select Graph &gt; Boundary Intensity. <br />
The Contour VOI Graph window (Figure 10) opens. This window displays a graph of the intensity values of the selected contour's boundary. <br />


==== Paint Grow dialog box options ====
=== Generating intensity graphs ===
Intensity profiles, or graphs, present information on the intensity values of the VOI region in an image. The intensity graph appears in the Intensity Graph window (Figure 11).<br />
 
'''To generate 2D intensity graphs'''<br />
1 Open an image.<br />
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br /><
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
Select VOI &gt; Graph in the MIPAV window and either of the following:<br />
* ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the VOI region. <br />
* ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
Right-click on the VOI and then select Graph and one of the following commands:<br />
* ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
* ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
* ''2.5D Total Intensity with Threshold'' -TBD. <br />
* ''2.5D Average Intensity with Threshold'' -TBD.<br />
The Intensity Graph window (Figure 11) opens.


{| border="1" cellpadding="5"
{| border="1" cellpadding="5"
|+ '''Figure 9. Paint Grow dialog box '''
|+ '''Figure 11. Intensity Graph window '''
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Cursor position and voxel intensity</font>'''</span></div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></div>
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<div class="CellBody">Indicates the coordinates and intensity of the pixel under the mouse pointer tip. This pixel is the seed point.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open Graph</font>'''</span>-Opens a PLT file that contains graph data.</div> <div class="CellBody">When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears. </div>
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[[Image:PaintGrow_StaticThreshold.jpg]]
[[Image:VOIGRaphMOdifyPointsVis.jpg]]
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Delta above selected voxel intensity</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Once a seed point has been selected, MIPAV uses this value to determine whether to fill adjacent voxels with color. The voxels that are filled must have intensity levels that fall within the range of the seed point intensity minus the lower delta value and the upper delta value. For example, if seed point has an intensity of 100.0, and the <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Delta Above Selected Pixel Intensity </font>''</span>value is 10 and the <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Delta Below Selected Pixel Intensity </font>''</span>value is 15, MIPAV color-fills adjacent voxels whose intensities range from 85.0 to 110.0.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Save Graph</font>'''</span>-Saves the graph data in a PLT file. </div> <div class="CellBody">When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Delta below selected voxel intensity</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Once a seed point is, MIPAV uses this value to determine whether to fill adjacent voxels with color. The voxels that are filled must have intensity levels that fall within the range of the seed point intensity minus the lower delta value and the upper delta value.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Parameters:</font>'''</span></div> <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Unrestricted size</font>'''</span></div> <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Maximum size</font>'''</span></div> <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Unrestricted distance</font>'''</span></div> <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Maximum distance</font>'''</span></div>
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<div class="CellBody">Constrains the growth of the paint grow operation. Select the <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Unrestricted size</font>'''</span> and <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Unrestricted distance</font>'''</span> check boxes to allow the paint grow operation to be applied without restraint. If the <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Unrestricted size</font>'''</span> check box is not selected, type the <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">maximum size</font>'''</span> (in cubic meters) of the paint grow region in the text box. If the <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Unrestricted distance</font>'''</span> check box is not selected, type the maximum distance from the original seed point in the text box.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Print Graph</font>'''</span>-Allows you to print the graph. When you select this command or press <br />Ctrl P, the Print dialog box opens.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Fuzzy connectedness</font>'''</span></div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Fuzzy connectedness</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Check tis box to use the fuzzy connectedness coefficient instead of static threshold. Here, Fuzzy connectedness represents the idea of connection or "hanging-togetherness" of image elements in an object by assigning a strength of connectedness to every possible path between every possible pair of image elements. </div> <div class="CellBody">A fuzzy connected object is defined with a fuzzy threshold or the strength of connectedness. </div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Close Graph</font>'''</span>-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Initial variance from selected VOI</font>'''</span></div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</font>'''</span></div>
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<div class="CellBody">Uses the initial intensity values from the selected region of interest (VOI).</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Delete Function</font>'''</span>-Allows you to delete the function that you select. However, you cannot delete a function if it is the only function displayed in the window.</div>
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[[Image:PaintGrow_FuzzyConnectedness.jpg]]
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Display fuzzy image</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Displays the result image in a separate frame. </div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Paste Function</font>'''</span>-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Fuzzy threshold</font>'''</span></div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Views</font>'''</span></div>
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<div class="CellBody">is a threshold on the strength of connectedness of image elements.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Modify Graph Features</font>'''</span>-Allows you to customize the appearance of the graph.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Close</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Closes this dialog box.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Range to Default</font>'''</span>-TBD.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Cancel</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Disregards any changes that you made in this dialog box and closes the dialog box.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Graph to Original</font>'''</span>-TBD.</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
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<div class="CellBody">Displays online help for this dialog box.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help Topics</font>'''</span>-Displays online help topics.</div>
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==== Examples of using the Paint Grow tool ====
'''To generate 3D intensity graphs of all slices in a dataset at a specific point'''<br />
 
1 Open an image.<br />
Here, is a step-by-step guide for selecting a region(s) of interest using the Paint Grow tool options. In this example we will use an image of the human eye and we will try to segment the blood vessels located on the retina.
2 Draw a point VOI on the image (Figure 12).<br />
First, make sure to adjust the contrast of your image so that the different tissues appear visually distinctive. For images with more than 8 bits per voxel you may want to use the various LUT available in MIPAV.<br />
3 Select the VOI.<br />
 
4 Do one of the following:<br />
'''To segment blood vessels using the static threshold'''<br />
*Select the Propagate VOI to all slices icon.<br />
1 Open the Paint Grow dialog box.<br />
*Select VOI &gt; Propagate &gt; To All Slices. <br />
2 Use the mouse cursor to select the point on the image (on a blood vessel) which has the desired intensity value.<br />
*Right-click on the VOI, then select Propagate &gt; To All Slices (Figure 12).<br />
3 Use the Change Paint Color option to select the color (other than red) which will be used for painting.<br />
5 Right-click on the VOI and select Show VOI Graph (Figure 12).<br />
4 On the Static Threshold tab, adjust the intensity thresholds so that the tissue you want to preserve is highlighted.<br />5 Check the Unrestricted size and Unrestricted distance options. This will allow the paint grow operation to be applied without restriction.<br />6 Watch the paint region growing.<br />
 
For example, when selecting the blood vessels, the image might look like the panel A for grayscale images or panel B for images after applying Blue LUT in the Figure 10 below.
 


{| border="1" cellpadding="5"
{| border="1" cellpadding="5"
|+ '''Figure 10. The Paint Grow tool was used to locate the blood vessels on the grayscale image (A) first, and then on the same image after applying the Blue LUT (B). '''
|+ '''Figure 12. Point VOI'''
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[[Image:RetinaVesselsGrayscale.jpg]]
|<div class="CellBody">A - the painted region appears in red (which is the default color)</div>
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[[Image:RetinaVessels BlueLUT.jpg]]
<div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div>
|<div class="CellBody">B - the painted region appears in green, because we selected it as a color contrast to LUT colors</div>
|[[Image:RetinaVeselsDialogOptions.jpg]]
|Dialog Options box
|}
'''To segment blood vessels using the Fuzzy Connectedness option'''<br />
1 Open an image of interest.<br />
2 You might consider to delineate a VOI on a region of the image which is of your interest, first. This is optional.<br />
1 Open the Paint Grow dialog box, and then open the Fuzzy Connectedness tab.<br />
2 Check the '''Fuzzy Connectedness''' check box to activate the tool.<br />
3 Check the '''Initial variance from selected VOI''' box (optional).<br />
4 Check the '''Display fuzzy image option''' to view the result in a new frame.<br />
5 Use the mouse cursor to select the point on the image (on a blood vessel) which has the desired intensity value.<br />
6 Adjust the Fuzzy thresholds so that the tissue you want to preserve is highlighted.<br />
7 Watch the paint region appeared in a new frame.<br />


For example, when selecting the blood vessels, the image might look like the panel A or panel B for images in the Figure 11 below.
<br clear="all" />


{| border="1" cellpadding="5"
{|
|+ '''Figure 11. The Fuzzy Connectedness option.'''
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[[Image:RetinaVesselsFuzzyGrayscale.jpg]]
|<div class="CellBody">a - the painted region appears in red </div>
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[[Image:RetinaVesselsFuzzyResult.jpg]]
|<div class="CellBody">b -the painted region also appears in a new frame</div>
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[[Image:RetinaVeselsDialogOptionsFuzzy.jpg]]
[[Image:PointVOIPropagate.jpg]]
|<div class="CellBody">c</div>
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'''To generate 3D intensity graphs of specific areas'''<br />
1 Open an image.<br />
2 Delineate a VOI on the image using the 3D rectangular VOI icon.<br />
3 Select the VOI. Then, do one of the following:<br />
*a Select VOI &gt; Graph and either of the following in the MIPAV window:<br />
** ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
** ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
*b Right-click the VOI, and then select Graph and one of the following commands in the MIPAV window:<br />
** ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
** ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
** ''2.5D Total Intensity with Threshold'' -TBD.<br />
** ''2.5D Average Intensity with Threshold'' -TBD.<br />
The Intensity Graph window (Figure 11) opens.<br />




[[Segmenting Images Using Contours and Masks:Converting VOI contours to masks]]
[[Customizing the appearance of graphs - Modify graph dialog box]]

Revision as of 20:22, 21 February 2012

MIPAV allows you to generate intensity profiles, or contour VOI graphs, for VOI contours. For delineated VOIs, you can generate 2D, 3D, or 4D intensity graphs. You can also generate a 3D intensity graph at a specific point across all slices in a dataset. For information on how to contour a VOI, refer to Chapter 1, "Segmenting Images Using Contours and Masks,"

Generating contour VOI graphs

Contour VOI graphs display the intensity values of the selected contour's boundary in the Contour VOI Graph window (Figure 10). You can generate either 2D or 3D contour VOI graphs.

To generate 2D contour VOI graphs
1 Open an image.
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.


Figure 10. Contour VOI Graph window

WindowContourVOIGraph.jpg

File
Open Graph-Opens a PLT file that contains graph data. When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears.
Save Graph-Saves the graph data in a PLT file. When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.
Print Graph-Allows you to print the graph. When you select this command or press
Ctrl P, the Print dialog box opens.
Close Graph-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.
Edit
Delete Function-Allows you to delete a specific function. However, you cannot delete a function if it is the only function displayed in the window.
Copy Function-Copies a function that is currently displayed in the window.
Paste Function-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.
Views
Modify Graph Features-Allows you to customize the appearance of the graph.
Reset Range to Default-[TBD]
Reset Graph to Original-[TBD].
Help
Help Topics-Displays online help topics.


3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:

  • Select VOI > Graph > Boundary Intensity in the MIPAV window.
  • Right click on the VOI and then select Graph > Boundary Intensity.
  • The Contour VOI Graph window (Figure 10) opens.

To generate 3D contour VOI graphs
1 Open an image.
2 Delineate a VOI on the image using the 3D rectangular VOI icon, in the MIPAV window.
3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:

  • Select VOI > Graph > Boundary Intensity in the MIPAV window.
  • Right-click on the VOI and then select Graph > Boundary Intensity.

The Contour VOI Graph window (Figure 10) opens. This window displays a graph of the intensity values of the selected contour's boundary.

Generating intensity graphs

Intensity profiles, or graphs, present information on the intensity values of the VOI region in an image. The intensity graph appears in the Intensity Graph window (Figure 11).

To generate 2D intensity graphs
1 Open an image.
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.
< 3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:
Select VOI > Graph in the MIPAV window and either of the following:

  • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the VOI region.
  • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.

Right-click on the VOI and then select Graph and one of the following commands:

  • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
  • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
  • 2.5D Total Intensity with Threshold -TBD.
  • 2.5D Average Intensity with Threshold -TBD.

The Intensity Graph window (Figure 11) opens.

Figure 11. Intensity Graph window
File
Open Graph-Opens a PLT file that contains graph data.
When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears.

VOIGRaphMOdifyPointsVis.jpg

Save Graph-Saves the graph data in a PLT file.
When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.
Print Graph-Allows you to print the graph. When you select this command or press
Ctrl P, the Print dialog box opens.
Close Graph-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.
Edit
Delete Function-Allows you to delete the function that you select. However, you cannot delete a function if it is the only function displayed in the window.
Paste Function-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.
Views
Modify Graph Features-Allows you to customize the appearance of the graph.
Reset Range to Default-TBD.
Reset Graph to Original-TBD.
Help
Help Topics-Displays online help topics.

To generate 3D intensity graphs of all slices in a dataset at a specific point
1 Open an image.
2 Draw a point VOI on the image (Figure 12).
3 Select the VOI.
4 Do one of the following:

  • Select the Propagate VOI to all slices icon.
  • Select VOI > Propagate > To All Slices.
  • Right-click on the VOI, then select Propagate > To All Slices (Figure 12).

5 Right-click on the VOI and select Show VOI Graph (Figure 12).

Figure 12. Point VOI


PointVOIPropagate.jpg

To generate 3D intensity graphs of specific areas
1 Open an image.
2 Delineate a VOI on the image using the 3D rectangular VOI icon.
3 Select the VOI. Then, do one of the following:

  • a Select VOI > Graph and either of the following in the MIPAV window:
    • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
    • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
  • b Right-click the VOI, and then select Graph and one of the following commands in the MIPAV window:
    • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
    • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
    • 2.5D Total Intensity with Threshold -TBD.
    • 2.5D Average Intensity with Threshold -TBD.

The Intensity Graph window (Figure 11) opens.


Customizing the appearance of graphs - Modify graph dialog box

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