View source for Delineating volumes of interest (VOIs)

== Delineating volumes of interest (VOIs) ==
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.

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. 

=== VOI types supported by MIPAV ===

*Point
*2D line
*Rectangular and square
*3D rectangular
*2D elliptical and circular
*Polygonal
*3D polygonal
*Interactive level-set

== Generating contour VOIs using predefined shapes ==

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]].

[[File:VoiToolbar.jpg|center|VOI toolbar]]

=== To generate contour VOIs using the predefined shapes ===

<ol>
<li>Select one of the contour icons from the VOI toolbar in the expanded MIPAV window.</li>
<li>Move the pointer to the image window. The pointer changes to a cross-hair shape. Do one of the following:</li>

<ul>
<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>
<li>'''For straight lines, rectangle (2D and 3D), and ellipsoid VOIs:''' position the cursor on the area where the contour should begin.
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>
<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>
<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. 
To complete a polyline, double-click the mouse button. To complete a polygon, connect the first and last nodes.</li>
</ul>
</ol>

'''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.

== Changing VOIs ==

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.

See also: [[FAQ: Trimming VOIs]].

=== To add a point and change the boundary of the VOI ===
[[File:exampleBoundaryRectangularVOI.jpg|350px|thumb|left|Adding a point and adjusting the boundary of a rectangular VOI]]

<ol>
<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> 
<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]].

'''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.

=== Adjusting VOI contour boundaries ===

After a contour is drawn, it might be necessary to adjust the boundaries so it more closely matches the VOI region.

==== To adjust VOI contours ====
<ol>
<li>Click a contour. The nodes become visible. </li>
<li>Select VOI &gt; Evolve boundary 2D &gt;Active Contour. The Evolve Boundary dialog box opens.</li>
<li>Modify the information in the window if necessary.</li>
<li>Click OK. A new contour, that more closely outlines the VOI, appears on the image. The old contour also remains.</li>
</ol>

See also: [[FAQ: Trimming VOIs]].

[[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"
|+ '''Evolve Boundary dialog box'''<br />
|-
|
<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">Enter values for X,Y, and Z directions which will be used to correct blurring. The default value is 2.0</div>

|-
|'''Resolution options'''
|If this box is checked, the algorithm uses the image resolution to normalize the Z scale. 
|-
|'''Evolve Boundary'''
|Replace Original Contour - the original VOI will be replaced with the new one.
|-
|'''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 />
Smoothness- enter the number from 0.5 to 2.4 to specify smoothness.
|-
|'''OK'''
|Applies the algorithm according to the specifications in this dialog box. 
|-
|'''Cancel'''
|Disregards any changes that you made in this dialog box and closes it.
|-
|'''Help'''
|TBD.
|}

== References ==
Software Tools for Brain MRI Segmentation, by Pierre-Louis Bazin [https://masi.vuse.vanderbilt.edu/vuiis/images/c/c5/Medic-software-2010.pdf PDF]

== 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]]
[[Category:Getting started]]