Generating graphs and Getting Started Quickly with MIPAV: Difference between pages

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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 />
== Getting Started Quickly with MIPAV ==
[[File:MipavSplash.gif|158px|thumb|right|MIPAV]]


=== Generating contour VOI graphs ===
This [http://mipav.cit.nih.gov/wiki/index.php/Main_Page#Documentation MIPAV WIKI] provides information to help you get started quickly using MIPAV. It explains basic tasks, such as starting and ending the program, opening and loading images, creating new images, and saving and printing images. In addition, it discusses how to create volumes of interest (VOIs), how to compare images using alphablending, and how to customize the program.
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 />


'''To generate 2D contour VOI graphs'''<br />
Sample images to start with MIPAV can be found here [[Sample images]].
1 Open an image.<br />
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br />


See also: [http://mipav.cit.nih.gov/pubwiki/index.php?title=MIPAV_change_list&oldid=39297 MIPAV change list].
=== [http://mipav.cit.nih.gov/wiki/index.php/Main_Page#Documentation Contents] ===
*[[Introducing MIPAV]]
*[[MIPAV mailing list]]
*[[Installing mipav#MipavNews|Viewing MIPAV News and Updates]]
*[[Supported Formats]]
*[[FAQ: Understanding Image Basics#FilesExtensions | Image files supported by MIPAV]]
*[[Installing mipav|Installing MIPAV]]
*[[MIPAV system requirements]]
*[[Installing mipav|Installing MIPAV]]
*[[Installing mipav#MipavUpgrade|Upgrading MIPAV]]
*[[Installing mipav#MipavUninstall|Uninstalling MIPAV]]
*[[Quitting MIPAV]]
*[[Allocating Memory in MIPAV]]
*[[Opening and loading image files]]
*[[MIPAV toolbars]]
*[[Displaying MIPAV Toolbars]]
*[[Displaying images]]
*[[Modifying image resolutions]]
*[[Changing Image Contrast]]
*[[Creating new images]]
*[[Saving and printing images]]
*[[Delineating volumes of interest (VOIs)| Volumes of Interest]]
*[[ImageJ | Working with ImageJ]]
*[[Customizing MIPAV]]
*[[Developing new tools using the API]]
*[[Technical Support | Contacting MIPAV support]]
Back to [http://mipav.cit.nih.gov/wiki/index.php/Main_Page#Documentation MIPAV WIKI]
<div id="StartingMIPAV"></div>
== Starting MIPAV ==
[[File:MIPAV_FirstAppear.jpg|450px|thumb|left|MIPAV: Main and Output windows]]
Starting MIPAV differs depending on your platform. To begin a MIPAV session, do the following:<br />


{| border="1" cellpadding="5"
{| border="1" cellpadding="5"
|+ '''Figure 10. Contour VOI Graph window '''
|+
|- bgcolor="#CCCCCC"
!
<div class="CellHeading">If your platform is . . .</div>
!
<div class="CellHeading">Then . . .</div>
|-
|-
| rowspan="1" colspan="3" |
|
[[Image:windowContourVOIGraph.jpg]]
<div class="CellBody">Windows 95, 98, 2000, NT, XP, Vista</div>
|
<div class="CellBody">Select Start &gt; Programs &gt; mipav &gt; mipav.</div>
|-
|-
| rowspan="4" colspan="1" |
|
<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">Linux</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">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>
<div class="CellBody">Open a shell. Go to the directory where you installed MIPAV, or the location you choose for the MIPAV links. At the prompt, type <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">./mipav</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">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>
<div class="CellBody">Mac Operating System (OSX)</div>
|-
|
| rowspan="1" colspan="2" |
<div class="CellBody">Unzip the installer. Double-click the installer icon on your desktop.</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>
|-
| 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>
|-
| rowspan="3" colspan="1" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</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">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>
|-
| rowspan="1" colspan="2" |
<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>
|-
| 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>
|-
| 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>
| 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>
|-
| 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>-<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>
<div class="CellBody">Unix OS (Sun Solaris, OS/2 Warp, and others</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>
<div class="CellBody">In a shell tool, command tool, or terminal window, go to the directory where you installed MIPAV. At the prompt, type <br /><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">./mipav</font>'''</span>.</div>
|}
|}


<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 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 />


=== Generating intensity graphs ===
Both the main Medical Image Processing, Analysis, &amp; Visualization (MIPAV) window and the Output window appear on your desktop. You can access most of [[Introducing MIPAV | MIPAV's features]] from [[Customizing MIPAV | the main menu bar]].
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 />
<div id="MipavMainWindow"></div>
1 Open an image.<br />
=== Main and Output windows options===
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 11. Intensity Graph window '''
|+ '''The Output window menu options'''<br />
|-
|'''File'''||
'''Save Messages'''-Saves all of the messages displayed on the currently open page (e.g., Global Data page, Data page, or Debug page). When you select this command, the Save dialog box opens.
'''Add tab'''- Adds a new tab to the Output window. When you select this option, the Add Tab dialog box opens. In this dialog box, enter the name for the new tab and press OK.
|-
|'''Edit'''
|'''Clear messages'''-Clears all of the messages that are displayed on the currently open page. Be sure that you want to use this command. There is no undo!
'''Copy'''-Copies the selected text on the currently open page. <br />
'''Cut'''-Removes the selected text from the currently open page. <br />
'''Select All'''-Selects all of the text on the currently open page.<br />
|-
| rowspan="1" colspan="2" |
'''The Output window toolbar'''
|-
|-
|
|
<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">Save Results</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>
<div class="CellBody">Saves all of the messages displayed on the currently open page. When you select this command, the Save dialog box opens.</div>
| rowspan="2" colspan="1" |
[[Image:VOIGRaphMOdifyPointsVis.jpg]]
|-
|-
|
|
<div class="CellBody"> </div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Copy</font>'''</span></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>
<div class="CellBody">Copies the selected text on the currently open page.</div>
|-
|-
|
|
<div class="CellBody"> </div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Paste</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">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>
<div class="CellBody">Pastes copied text into the currently open page at the cursor point.</div>
|-
|-
|
|
<div class="CellBody"> </div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Cut</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">Close Graph</font>'''</span>-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.</div>
<div class="CellBody">Removes the selected text from the currently open page.</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>
<div class="CellBody">'''Remove selected tab'''</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">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>
<div class="CellBody">Removes selected tab from the output window.</div>
|-
|-
|
<div class="CellBody"> </div>
| rowspan="1" colspan="2" |
| 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>
<div class="CellBody">'''The Output window default tabs'''</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>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Data tab</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>
|-
|
|
<div class="CellBody"> </div>
<div class="CellBody">Displays messages that apply to the currently active image.</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>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Debug tab</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>-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>
<div class="CellBody">Displays debugging information for the currently selected image.</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 />
<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"
After starting MIPAV, you can open and load image files, create new images, access DICOM images, customize MIPAV, and end the session.
|+ '''Figure 12. Point VOI'''
 
|-
<div id="ManagingMemoryResources"></div>
|
<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" />
== Managing memory resources ==


{|
MIPAV requires at least 35 Mb of random access memory (RAM). Additional memory is needed to correctly display image files and to quantify the data. To determine the amount of additional memory needed, multiply the size of the image file that you want to display by 10. Thus, if an image file is 2 Mb, you must allocate an additional 20 Mb of RAM (in addition to the base of 35 Mb) for it to display correctly. Because memory requirements fluctuate depending on the size and number of image files open, it may be necessary to allocate additional memory during a session. Refer to [[FAQ: Understanding Memory]] for more examples on required memory calculations.
|
[[Image:PointVOIPropagate.jpg]]
|}


'''To generate 3D intensity graphs of specific areas'''<br />
For more information, refer to: [[Allocating Memory in MIPAV]] and [[FAQ: Understanding Memory]].
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: ==
*[[Sample images]]
*[[Allocating Memory in MIPAV]]
*[[Opening and loading image files]]
*[[MIPAV toolbars]]
*[[Displaying images]]
*[[FAQ: Understanding Memory]]
*[[FAQ: Customizing MIPAV]]
*[[FAQ: Understanding Image Basics]]
*[[FAQ: Understanding Changes in MIPAV]]


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

Revision as of 14:33, 4 June 2015

Getting Started Quickly with MIPAV

MIPAV

This MIPAV WIKI provides information to help you get started quickly using MIPAV. It explains basic tasks, such as starting and ending the program, opening and loading images, creating new images, and saving and printing images. In addition, it discusses how to create volumes of interest (VOIs), how to compare images using alphablending, and how to customize the program.

Sample images to start with MIPAV can be found here Sample images.

See also: MIPAV change list.

Contents

Back to MIPAV WIKI

Starting MIPAV

MIPAV: Main and Output windows

Starting MIPAV differs depending on your platform. To begin a MIPAV session, do the following:

If your platform is . . .
Then . . .
Windows 95, 98, 2000, NT, XP, Vista
Select Start > Programs > mipav > mipav.
Linux
Open a shell. Go to the directory where you installed MIPAV, or the location you choose for the MIPAV links. At the prompt, type ./mipav.
Mac Operating System (OSX)
Unzip the installer. Double-click the installer icon on your desktop.
Unix OS (Sun Solaris, OS/2 Warp, and others
In a shell tool, command tool, or terminal window, go to the directory where you installed MIPAV. At the prompt, type
./mipav.


Both the main Medical Image Processing, Analysis, & Visualization (MIPAV) window and the Output window appear on your desktop. You can access most of MIPAV's features from the main menu bar.

Main and Output windows options

The Output window menu options
File

Save Messages-Saves all of the messages displayed on the currently open page (e.g., Global Data page, Data page, or Debug page). When you select this command, the Save dialog box opens. Add tab- Adds a new tab to the Output window. When you select this option, the Add Tab dialog box opens. In this dialog box, enter the name for the new tab and press OK.

Edit Clear messages-Clears all of the messages that are displayed on the currently open page. Be sure that you want to use this command. There is no undo!

Copy-Copies the selected text on the currently open page.
Cut-Removes the selected text from the currently open page.
Select All-Selects all of the text on the currently open page.

The Output window toolbar

Save Results
Saves all of the messages displayed on the currently open page. When you select this command, the Save dialog box opens.
Copy
Copies the selected text on the currently open page.
Paste
Pastes copied text into the currently open page at the cursor point.
Cut
Removes the selected text from the currently open page.
Remove selected tab
Removes selected tab from the output window.
The Output window default tabs
Data tab
Displays messages that apply to the currently active image.
Debug tab
Displays debugging information for the currently selected image.


After starting MIPAV, you can open and load image files, create new images, access DICOM images, customize MIPAV, and end the session.

Managing memory resources

MIPAV requires at least 35 Mb of random access memory (RAM). Additional memory is needed to correctly display image files and to quantify the data. To determine the amount of additional memory needed, multiply the size of the image file that you want to display by 10. Thus, if an image file is 2 Mb, you must allocate an additional 20 Mb of RAM (in addition to the base of 35 Mb) for it to display correctly. Because memory requirements fluctuate depending on the size and number of image files open, it may be necessary to allocate additional memory during a session. Refer to FAQ: Understanding Memory for more examples on required memory calculations.

For more information, refer to: Allocating Memory in MIPAV and FAQ: Understanding Memory.

See also:

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