Delineating volumes of interest (VOIs) and Generating graphs: Difference between pages

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== Delineating volumes of interest (VOIs) ==
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 />
MIPAV povides tools that allow you to automatically, semiautomatically, and manually identify and modify volumes of interest (VOIs). <br />
'''Volume of interest (VOI)''' is the portion of the image in the dataset on which you want to focus. It may be either one slice or multiple slices throughout the dataset.<br />


Each VOI can be formed from multiple contours in a single slice or multiple slices. Once an object is segmented and defined by a VOI, [[Calculating VOI statistics |statistics of the volume]] can be calculated.
=== 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. <br />


MIPAV supports over 32,000 unique VOIs on a single dataset. Additionally, you can move or delete nodes on the VOI and add new points.  
'''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 />


=== VOI types supported by MIPAV ===


*Point
{| border="1" cellpadding="5"
*2D line
|+ '''Figure 10. Contour VOI Graph window '''
*Rectangular and square
|-
*3D rectangular
| rowspan="1" colspan="3" |
*2D elliptical and circular
[[Image:windowContourVOIGraph.jpg]]
*Polygonal
|-
*3D polygonal
| rowspan="4" colspan="1" |
*Interactive level-set
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></div>
 
| rowspan="1" colspan="2" |
== Generating contour VOIs using predefined shapes ==
<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>
 
|-
MIPAV includes icons of predefined shapes, such as points, lines, ellipses, or rectangles, that you can use to create VOIs. These icons are on the VOI toolbar. See also: [[MIPAV toolbars#VoiToolbar| VOI toolbar]] and [[Displaying MIPAV Toolbars]].
| rowspan="1" colspan="2" |
 
<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>
[[File:VoiToolbar.jpg|center|VOI toolbar]]
|-
 
| rowspan="1" colspan="2" |
=== To generate contour VOIs using the predefined shapes ===
<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>
 
|-
<ol>
| rowspan="1" colspan="2" |
<li>Select one of the contour icons from the VOI toolbar in the expanded MIPAV window.</li>
<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>
<li>Move the pointer to the image window. The pointer changes to a cross-hair shape. Do one of the following:</li>
|-
 
| rowspan="3" colspan="1" |
<ul>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</font>'''</span></div>
<li>'''For point and levelset VOIs:''' Position the cursor on the area where the point or levelset should be drawn. Click the mouse button.</li>
| rowspan="1" colspan="2" |
<li>'''For straight lines, rectangle (2D and 3D), and ellipsoid VOIs:''' position the cursor on the area where the contour should begin.
<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>
Click the mouse button. While holding down the mouse button, drag the cursor until the contour is the desired size.</li>
|-
<li>You create '''a square VOI''' using the VOI rectangle tool while holding down the CTRL key. The square length can also be directly edited by the user by clicking the right mouse button.</li>
| rowspan="1" colspan="2" |
<li>You can also create '''a circular VOI''' by pressing the elliptical VOI icon while holding down the CTRL key. The circle diameter can be directly edited by clicking the right mouse button and calling VOI properties menu. </li>
<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>
<li>'''For polyline and  polygon VOIs:''' position the cursor over the area where the contour should begin.  
|-
Click the mouse button. A point appears. Alternate between moving the mouse and selecting the mouse button to outline the VOI.
| rowspan="1" colspan="2" |
To complete a polyline, double-click the mouse button. To complete a polygon, connect the first and last nodes.</li>
<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>
</ul>
|-
</ol>
| rowspan="3" colspan="1" |
 
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Views</font>'''</span></div>
'''Tip:''' To draw the same shape several times in succession, hold down the Shift key while you select the applicable icon from the VOI toolbar and draw.
| rowspan="1" colspan="2" |
 
<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>
== Changing VOIs ==
|-
 
| rowspan="1" colspan="2" |
No matter which method was chosen to delineate a VOI, you can add VOI points and change the boundaries of the VOI. For example, suppose you created a VOI on an image with using the Rectangle VOI option. If you notice that a part of the image that should be included in the VOI is not included, the boundary of the rectangle needs to be adjusted to include the missing portion of the image.
<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>
|-
| rowspan="1" colspan="2" |
<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>
|-
|
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
| rowspan="1" colspan="2" |
<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>
|}


See also: [[FAQ: Trimming VOIs]].
<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 />


=== To add a point and change the boundary of the VOI ===
'''To generate 3D contour VOI graphs'''<br />
[[File:exampleBoundaryRectangularVOI.jpg|350px|thumb|left|Adding a point and adjusting the boundary of a rectangular VOI]]
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 />


<ol>
=== Generating intensity graphs ===
<li>[[Image:crosshairBlack.jpg]] Select the VOI. Notice that white points appear at the corners of the VOI and a small cross appears in the middle of the VOI.</li>
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 />
<li> Place the cursor on the portion of the VOI you want to adjust. The cursor changes from a cross to a hand [[Image:HandPointer.jpg]].</li> 
<li> Click once. A white point appears on the line.</li>
<li>Select the point and drag it to include the missing part of the image.</li>
</ol>


See also: [[FAQ: Trimming VOIs]].
'''To generate 2D intensity graphs'''<br />
 
1 Open an image.<br />
'''Tip:''' Circular VOIs are composed of a continuous series of points around the diameter of the circle. You only need to select one of those points and drag it to enlarge the circle.
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br /><
 
3 Select the VOI. <br />
=== Adjusting VOI contour boundaries ===
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 />
After a contour is drawn, it might be necessary to adjust the boundaries so it more closely matches the VOI region.
*To Previous Slice<br />
 
*To All Slices<br />
==== To adjust VOI contours ====
4 Do one of the following:<br />
<ol>
Select VOI &gt; Graph in the MIPAV window and either of the following:<br />
<li>Click a contour. The nodes become visible. </li>
* ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the VOI region. <br />
<li>Select VOI &gt; Evolve boundary 2D &gt;Active Contour. The Evolve Boundary dialog box opens.</li>
* ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
<li>Modify the information in the window if necessary.</li>
Right-click on the VOI and then select Graph and one of the following commands:<br />
<li>Click OK. A new contour, that more closely outlines the VOI, appears on the image. The old contour also remains.</li>
* ''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 />
</ol>
* ''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 />
See also: [[FAQ: Trimming VOIs]].
* ''2.5D Average Intensity with Threshold'' -TBD.<br />
 
The Intensity Graph window (Figure 11) opens.
[[File:VoiEvolveBoundaryManual.jpg|200px|thumb|right|The Evolve Boundary dialog box - user defined boundary options]]
==== Deleting VOI contours ====
[[Image:iconCutSelectedContour.jpg]] To delete an old contour, select the contour, and then select Cut Selected Contour, or press the Del key on the keyboard.
 
==== To "manually" evolve 2D VOI boundaries ====
<ol>
<li>Click a contour. The nodes become visible. </li>
<li>From the main MIPAV menu select VOI &gt; Evolve boundary 2D &gt;User-defined. The Evolve Boundary dialog box opens.</li>
<li>In the '''Enter size change''' field, specify the amount to shrink/grow a contour in image units (i.e., mm).</li>
<li>Click OK. A new contour appears on the image.</li>
</ol>
 
== Evolve VOI Boundary dialog box ==
[[File:EvolveBoundary.jpg|350px|thumb|left|The Evolve VOI Boundary dialog box]]


{| border="1" cellpadding="5"
{| border="1" cellpadding="5"
|+ '''Evolve Boundary dialog box'''<br />
|+ '''Figure 11. Intensity Graph window '''
|-
|
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></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>
| rowspan="2" colspan="1" |
[[Image:VOIGRaphMOdifyPointsVis.jpg]]
|-
|-
|
|
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Scale of the Gaussian</font>'''</span></div>
<div class="CellBody"> </div>
|
|
<div class="CellBody">Enter values for X,Y, and Z directions which will be used to correct blurring. The default value is 2.0</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>
 
|-
|-
|'''Resolution options'''
|
|If this box is checked, the algorithm uses the image resolution to normalize the Z scale.  
<div class="CellBody"> </div>
| rowspan="1" colspan="2" |
<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>
|-
|-
|'''Evolve Boundary'''
|
|Replace Original Contour - the original VOI will be replaced with the new one.
<div class="CellBody"> </div>
| rowspan="1" colspan="2" |
<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>
|-
|-
|'''Algorithm parameters'''
|
| Move Boundary - depending on the selected option, the VOI will be moved in 1) any direction, 2) only inward, 3) only outward.<br /> Boundary Iterations- specify the number of iterations needed to calculate the new boundary.<br />
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</font>'''</span></div>
Smoothness- enter the number from 0.5 to 2.4 to specify smoothness.
| rowspan="1" colspan="2" |
<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>
|-
|-
|'''OK'''
|
|Applies the algorithm according to the specifications in this dialog box.  
<div class="CellBody"> </div>
| rowspan="1" colspan="2" |
<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>
|-
|-
|'''Cancel'''
|
|Disregards any changes that you made in this dialog box and closes it.
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Views</font>'''</span></div>
| rowspan="1" colspan="2" |
<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>
|-
|-
|'''Help'''
|
|TBD.
<div class="CellBody"> </div>
| rowspan="1" colspan="2" |
<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>
|-
|
<div class="CellBody"> </div>
| rowspan="1" colspan="2" |
<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>
|-
|
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
| rowspan="1" colspan="2" |
<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>
|}
 
'''To generate 3D intensity graphs of all slices in a dataset at a specific point'''<br />
1 Open an image.<br />
2 Draw a point VOI on the image (Figure 12).<br />
3 Select the VOI.<br />
4 Do one of the following:<br />
*Select the Propagate VOI to all slices icon.<br />
*Select VOI &gt; Propagate &gt; To All Slices. <br />
*Right-click on the VOI, then select Propagate &gt; To All Slices (Figure 12).<br />
5 Right-click on the VOI and select Show VOI Graph (Figure 12).<br />
 
{| border="1" cellpadding="5"
|+ '''Figure 12. Point VOI'''
|-
|
<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>
 
<br clear="all" />
 
{|
|
[[Image:PointVOIPropagate.jpg]]
|}
|}


== References ==
'''To generate 3D intensity graphs of specific areas'''<br />
Software Tools for Brain MRI Segmentation, by Pierre-Louis Bazin [https://masi.vuse.vanderbilt.edu/vuiis/images/c/c5/Medic-software-2010.pdf PDF]
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 />


== See also: ==
*[[FAQ: Trimming VOIs]]
*[[Calculating VOI statistics]]
*[[Reviewing the statistics]]
*[[Reviewing the statistics|Generating graphs (intensity profiles)]] 
*[[Reviewing the statistics|Saving and printing images]]


[[Category:Help]]
[[Customizing the appearance of graphs - Modify graph dialog box]]
[[Category:Getting started]]

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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