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	<id>https://www.slicer.org/w/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Tgl</id>
	<title>Slicer Wiki - User contributions [en]</title>
	<link rel="self" type="application/atom+xml" href="https://www.slicer.org/w/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Tgl"/>
	<link rel="alternate" type="text/html" href="https://www.slicer.org/wiki/Special:Contributions/Tgl"/>
	<updated>2026-04-30T08:17:24Z</updated>
	<subtitle>User contributions</subtitle>
	<generator>MediaWiki 1.33.0</generator>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10287</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10287"/>
		<updated>2009-07-30T02:43:13Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings (defaults to /Users/$USER/Slicer3$USER on a Mac)&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (for example, /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* After download and install of the new extension,  ExtensionsInstallPath/@SVN@/$ExtensionName is added to the Application's ModulePaths.&lt;br /&gt;
*  @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
* On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10286</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10286"/>
		<updated>2009-07-30T02:41:11Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings (defaults to /Users/$USER/Slicer3$USER on a Mac)&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (for example, /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
&lt;br /&gt;
Extension manager will store to ExtensionsInstallPath/@SVN@  Where @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
&lt;br /&gt;
This path is appended to PotentialModulePaths. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10285</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10285"/>
		<updated>2009-07-30T02:40:42Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings (defaults to /Users/$USER/Slicer3$USER on a Mac)&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Unarchive to TemporaryDirectory/extension before moving to final install path&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
&lt;br /&gt;
Extension manager will store to ExtensionsInstallPath/@SVN@  Where @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
&lt;br /&gt;
This path is appended to PotentialModulePaths. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10284</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10284"/>
		<updated>2009-07-30T02:40:20Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Unarchive to TemporaryDirectory/extension before moving to final install path&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
&lt;br /&gt;
Extension manager will store to ExtensionsInstallPath/@SVN@  Where @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
&lt;br /&gt;
This path is appended to PotentialModulePaths. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10277</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10277"/>
		<updated>2009-07-28T19:43:46Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Unarchive to TemporaryDirectory/extension before moving to final install path&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
&lt;br /&gt;
Extension manager will store to ExtensionsInstallPath/@SVN@  Where @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
&lt;br /&gt;
This path is appended to PotentialModulePaths. &lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
&lt;br /&gt;
On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10276</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10276"/>
		<updated>2009-07-28T19:23:02Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
&lt;br /&gt;
Extension manager will store to ExtensionsInstallPath/@SVN@  Where @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
&lt;br /&gt;
This path is appended to PotentialModulePaths. &lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
&lt;br /&gt;
On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10275</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10275"/>
		<updated>2009-07-28T19:22:50Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
&lt;br /&gt;
Extension manager will store to ExtensionsInstallPath/@SVN@  Where @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
&lt;br /&gt;
This path is appended to PotentialModulePaths. &lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
 On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10274</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10274"/>
		<updated>2009-07-28T18:23:58Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
&lt;br /&gt;
Extension manager will store to ExtensionsInstallPath/@SVN@  Where @SVN@ is the svn revision number of the repository from Slicer3Version.txt for the build.&lt;br /&gt;
&lt;br /&gt;
This path is appended to PotentialModulePaths.  On startup, Slicer3 will search all potential module paths, substituting @SVN@ with the value recorded in Slicer3Version.txt&lt;br /&gt;
&lt;br /&gt;
TODO:&lt;br /&gt;
Check all subdirectories of the ExtensionsInstallPath and see if a previous version had downloaded an extension and if it's not available in the current version, then query the user to download it.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10273</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10273"/>
		<updated>2009-07-28T18:07:18Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionsInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionsInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10272</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10272"/>
		<updated>2009-07-28T18:01:29Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
* Zip files downloaded to TemporaryDirectory&lt;br /&gt;
* Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
* Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10271</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10271"/>
		<updated>2009-07-28T18:01:18Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
&lt;br /&gt;
'''ExtensionInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
 * Zip files downloaded to TemporaryDirectory&lt;br /&gt;
 * Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
 * Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10270</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10270"/>
		<updated>2009-07-28T18:01:05Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''TemporaryDirectory''' is user-defined via Application Settings, defaults to /Users/$USER/Slicer3$USER&lt;br /&gt;
'''ExtensionInstallPath''' is user-defined via Application Settings,  defaults to value of TemporaryDirectory if not set by user&lt;br /&gt;
  &lt;br /&gt;
 * Zip files downloaded to TemporaryDirectory&lt;br /&gt;
 * Extensions installed to Slicer3 SVN Revision-based subdirectory of ExtensionInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
 * Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10269</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10269"/>
		<updated>2009-07-28T17:58:58Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;  Zip files downloaded to TemporaryDirectory (default: /Users/$USER/Slicer3$USER)&lt;br /&gt;
  Extensions installed to ExtensionInstallPath (default: /Users/$USER/Slicer3$USER/@SVN@)&lt;br /&gt;
  Slicer3 &amp;quot;default&amp;quot; extensions in Slicer3_INSTALL_MODULES_LIB_DIR&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10268</id>
		<title>Slicer3:Extensions:Directories</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:Directories&amp;diff=10268"/>
		<updated>2009-07-28T17:29:51Z</updated>

		<summary type="html">&lt;p&gt;Tgl: New page: TemporaryDirectory /Users/$USER/Slicer3$USER ExtensionsInstallPath $TemporaryDirectory/$SLICER_SVN_REVISION Slicer3 &amp;quot;installed&amp;quot; extensions $Slicer3_INSTALL_MODULES_LIB_DIR Extension&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;TemporaryDirectory /Users/$USER/Slicer3$USER&lt;br /&gt;
ExtensionsInstallPath $TemporaryDirectory/$SLICER_SVN_REVISION&lt;br /&gt;
Slicer3 &amp;quot;installed&amp;quot; extensions $Slicer3_INSTALL_MODULES_LIB_DIR&lt;br /&gt;
Extension&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9875</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9875"/>
		<updated>2009-06-23T19:10:58Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* 2009 Summer Project Week */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
** ModulePaths&lt;br /&gt;
** ModuleCachePath&lt;br /&gt;
** ExtensionDownloadDirectory&lt;br /&gt;
** ???&lt;br /&gt;
* ApplicationSettings&lt;br /&gt;
** relabel &amp;quot;Module Cache Path&amp;quot; to &amp;quot;Extensions Install Directory&amp;quot;&lt;br /&gt;
** use Temporary Directory as the download location for zip files&lt;br /&gt;
&lt;br /&gt;
== 2009 Summer Project Week ==&lt;br /&gt;
&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
  r9763 | tgl | 2009-06-23 11:04:34 -0400 (Tue, 23 Jun 2009) | 1 line&lt;br /&gt;
  Changed paths:&lt;br /&gt;
     M /trunk/Applications/GUI/Slicer3.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesConfigurationStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.h&lt;br /&gt;
  &lt;br /&gt;
  ENH rename ModuleCachePath to ExtensionsInstallPath&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
  r9766 | tgl | 2009-06-23 11:49:19 -0400 (Tue, 23 Jun 2009) | 1 line&lt;br /&gt;
  Changed paths:&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.h&lt;br /&gt;
  &lt;br /&gt;
  ENH remove ExtensionsDownloadDirectory, obsolete, use TemporaryDirectory&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
  r9771 | tgl | 2009-06-23 15:07:28 -0400 (Tue, 23 Jun 2009) | 1 line&lt;br /&gt;
  Changed paths:&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.cxx&lt;br /&gt;
  &lt;br /&gt;
  BUG set potential module paths, enabling the new modules&lt;br /&gt;
  ------------------------------------------------------------------------&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9874</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9874"/>
		<updated>2009-06-23T15:49:57Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* 2009 Summer Project Week */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
** ModulePaths&lt;br /&gt;
** ModuleCachePath&lt;br /&gt;
** ExtensionDownloadDirectory&lt;br /&gt;
** ???&lt;br /&gt;
* ApplicationSettings&lt;br /&gt;
** relabel &amp;quot;Module Cache Path&amp;quot; to &amp;quot;Extensions Install Directory&amp;quot;&lt;br /&gt;
** use Temporary Directory as the download location for zip files&lt;br /&gt;
&lt;br /&gt;
== 2009 Summer Project Week ==&lt;br /&gt;
&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
  r9763 | tgl | 2009-06-23 11:04:34 -0400 (Tue, 23 Jun 2009) | 1 line&lt;br /&gt;
  Changed paths:&lt;br /&gt;
     M /trunk/Applications/GUI/Slicer3.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesConfigurationStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.h&lt;br /&gt;
  &lt;br /&gt;
  ENH rename ModuleCachePath to ExtensionsInstallPath&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
  r9766 | tgl | 2009-06-23 11:49:19 -0400 (Tue, 23 Jun 2009) | 1 line&lt;br /&gt;
  Changed paths:&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.h&lt;br /&gt;
  &lt;br /&gt;
  ENH remove ExtensionsDownloadDirectory, obsolete, use TemporaryDirectory&lt;br /&gt;
  ------------------------------------------------------------------------&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9873</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9873"/>
		<updated>2009-06-23T15:05:51Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* 2009 Summer Project Week */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
** ModulePaths&lt;br /&gt;
** ModuleCachePath&lt;br /&gt;
** ExtensionDownloadDirectory&lt;br /&gt;
** ???&lt;br /&gt;
* ApplicationSettings&lt;br /&gt;
** relabel &amp;quot;Module Cache Path&amp;quot; to &amp;quot;Extensions Install Directory&amp;quot;&lt;br /&gt;
** use Temporary Directory as the download location for zip files&lt;br /&gt;
&lt;br /&gt;
== 2009 Summer Project Week ==&lt;br /&gt;
&lt;br /&gt;
  ------------------------------------------------------------------------&lt;br /&gt;
  r9763 | tgl | 2009-06-23 11:04:34 -0400 (Tue, 23 Jun 2009) | 1 line&lt;br /&gt;
  Changed paths:&lt;br /&gt;
     M /trunk/Applications/GUI/Slicer3.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplication.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.h&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesConfigurationStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.cxx&lt;br /&gt;
     M /trunk/Base/GUI/vtkSlicerModulesStep.h&lt;br /&gt;
  &lt;br /&gt;
  ENH rename ModuleCachePath to ExtensionsInstallPath&lt;br /&gt;
  ------------------------------------------------------------------------&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9872</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9872"/>
		<updated>2009-06-23T15:05:27Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* 2009 Summer Project Week */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
** ModulePaths&lt;br /&gt;
** ModuleCachePath&lt;br /&gt;
** ExtensionDownloadDirectory&lt;br /&gt;
** ???&lt;br /&gt;
* ApplicationSettings&lt;br /&gt;
** relabel &amp;quot;Module Cache Path&amp;quot; to &amp;quot;Extensions Install Directory&amp;quot;&lt;br /&gt;
** use Temporary Directory as the download location for zip files&lt;br /&gt;
&lt;br /&gt;
== 2009 Summer Project Week ==&lt;br /&gt;
&lt;br /&gt;
------------------------------------------------------------------------&lt;br /&gt;
r9763 | tgl | 2009-06-23 11:04:34 -0400 (Tue, 23 Jun 2009) | 1 line&lt;br /&gt;
Changed paths:&lt;br /&gt;
   M /trunk/Applications/GUI/Slicer3.cxx&lt;br /&gt;
   M /trunk/Base/GUI/vtkSlicerApplication.cxx&lt;br /&gt;
   M /trunk/Base/GUI/vtkSlicerApplication.h&lt;br /&gt;
   M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.cxx&lt;br /&gt;
   M /trunk/Base/GUI/vtkSlicerApplicationSettingsInterface.h&lt;br /&gt;
   M /trunk/Base/GUI/vtkSlicerModulesConfigurationStep.cxx&lt;br /&gt;
   M /trunk/Base/GUI/vtkSlicerModulesStep.cxx&lt;br /&gt;
   M /trunk/Base/GUI/vtkSlicerModulesStep.h&lt;br /&gt;
&lt;br /&gt;
ENH rename ModuleCachePath to ExtensionsInstallPath&lt;br /&gt;
------------------------------------------------------------------------&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9871</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9871"/>
		<updated>2009-06-23T14:44:16Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
** ModulePaths&lt;br /&gt;
** ModuleCachePath&lt;br /&gt;
** ExtensionDownloadDirectory&lt;br /&gt;
** ???&lt;br /&gt;
* ApplicationSettings&lt;br /&gt;
** relabel &amp;quot;Module Cache Path&amp;quot; to &amp;quot;Extensions Install Directory&amp;quot;&lt;br /&gt;
** use Temporary Directory as the download location for zip files&lt;br /&gt;
&lt;br /&gt;
== 2009 Summer Project Week ==&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9784</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9784"/>
		<updated>2009-06-16T14:04:18Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
** ModulePaths&lt;br /&gt;
** ModuleCachePath&lt;br /&gt;
** ExtensionDownloadDirectory&lt;br /&gt;
** ???&lt;br /&gt;
* ApplicationSettings&lt;br /&gt;
** relabel &amp;quot;Module Cache Path&amp;quot; to &amp;quot;Extensions Install Directory&amp;quot;&lt;br /&gt;
** use Temporary Directory as the download location for zip files&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9783</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9783"/>
		<updated>2009-06-16T13:59:14Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
** ModulePaths&lt;br /&gt;
** ModuleCachePath&lt;br /&gt;
** ExtensionDownloadDirectory&lt;br /&gt;
** ???&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9782</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9782"/>
		<updated>2009-06-16T13:58:55Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;br /&gt;
* define all paths&lt;br /&gt;
-- ModulePaths&lt;br /&gt;
-- ModuleCachePath&lt;br /&gt;
-- ExtensionDownloadDirectory&lt;br /&gt;
-- ???&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9781</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9781"/>
		<updated>2009-06-16T13:56:59Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot; in ModulesPath&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9780</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9780"/>
		<updated>2009-06-16T13:56:29Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;br /&gt;
* &amp;quot;Slicer3-install-bin/../lib/Slicer3/Modules&amp;quot;&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9779</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9779"/>
		<updated>2009-06-16T13:52:13Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add vtkSlicerApplication::ModulePaths if found downloaded extensions are not there&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9778</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9778"/>
		<updated>2009-06-16T13:48:47Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;br /&gt;
* add ::ModulePaths if found downloaded extensions are not there&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9777</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9777"/>
		<updated>2009-06-16T13:44:20Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;br /&gt;
* what happens when the Desktop is used as the &amp;quot;module cache path&amp;quot;&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9776</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9776"/>
		<updated>2009-06-16T13:39:21Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;br /&gt;
* check that ModulePaths disable/enable is not inadvertantly set&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9775</id>
		<title>Slicer3:Extensions:TODO-2009-06-16</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions:TODO-2009-06-16&amp;diff=9775"/>
		<updated>2009-06-16T13:38:44Z</updated>

		<summary type="html">&lt;p&gt;Tgl: New page: * search vtkSlicerApplication::ModulePaths when consructing the installed extension listings * warn user if cache path is not writable&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* search vtkSlicerApplication::ModulePaths when consructing the installed extension listings&lt;br /&gt;
* warn user if cache path is not writable&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Modules:ExtensionsManagementWizard-Documentation-3.4&amp;diff=9500</id>
		<title>Modules:ExtensionsManagementWizard-Documentation-3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Modules:ExtensionsManagementWizard-Documentation-3.4&amp;diff=9500"/>
		<updated>2009-05-08T21:30:39Z</updated>

		<summary type="html">&lt;p&gt;Tgl: Modules::ExtensionsManagementWizard-Documentation-3.4 moved to Modules:ExtensionsManagementWizard-Documentation-3.4&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Placeholder for description of the Extensions Management Wizard in 3.4&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Modules::ExtensionsManagementWizard-Documentation-3.4&amp;diff=9501</id>
		<title>Modules::ExtensionsManagementWizard-Documentation-3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Modules::ExtensionsManagementWizard-Documentation-3.4&amp;diff=9501"/>
		<updated>2009-05-08T21:30:39Z</updated>

		<summary type="html">&lt;p&gt;Tgl: Modules::ExtensionsManagementWizard-Documentation-3.4 moved to Modules:ExtensionsManagementWizard-Documentation-3.4&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;#REDIRECT [[Modules:ExtensionsManagementWizard-Documentation-3.4]]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9499</id>
		<title>Slicer3:Extensions</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9499"/>
		<updated>2009-05-08T21:29:52Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* FOR DEVELOPERS */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;3D Slicer now supports extensions.  Extensions are available from an extension server.  This allows end-users to select the extensions useful to them, without having to download the entire extension archive.&lt;br /&gt;
&lt;br /&gt;
== FOR DEVELOPERS ==&lt;br /&gt;
&lt;br /&gt;
Extensions must follow the appropriate architecture for them to be made available to end users.  See [[Slicer3:Loadable_Modules]] for an example of how to make GUI and GUI-less Loadable Modules.  Command Line and Scripted Modules will also work with this framework.&lt;br /&gt;
&lt;br /&gt;
To enable your Command Line, Scripted, or Loadable module, add an &amp;quot;s3ext&amp;quot; script to the /Slicer3/Extensions directory of the source repository:&lt;br /&gt;
&lt;br /&gt;
PythonSampleScriptedModule.s3ext:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
#&lt;br /&gt;
# first token of each non-comment line is the keyword and the rest of the line &lt;br /&gt;
# (including spaces) is the value.&lt;br /&gt;
# - the value can be blank&lt;br /&gt;
#&lt;br /&gt;
&lt;br /&gt;
# scm is source code manager (i.e. svn)&lt;br /&gt;
scm       svn&lt;br /&gt;
svnpath   https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules/Scripted/PythonSampleScriptedModule&lt;br /&gt;
svnusername slicerbot&lt;br /&gt;
svnpassword slicer&lt;br /&gt;
&lt;br /&gt;
# list dependencies &lt;br /&gt;
# - these should be names of other modules that have .s3ext files &lt;br /&gt;
# - the dependencies will be built first&lt;br /&gt;
depends ScriptedModule&lt;br /&gt;
&lt;br /&gt;
# homepage&lt;br /&gt;
homepage  http://www.slicer.org&lt;br /&gt;
&lt;br /&gt;
# match category in the xml description of the module (where it shows up in Modules menu)&lt;br /&gt;
category  Developer Tools&lt;br /&gt;
&lt;br /&gt;
# give people an idea what to expect from this code &lt;br /&gt;
# - is it just a test or something you stand beind?&lt;br /&gt;
status    Beta&lt;br /&gt;
&lt;br /&gt;
# One line description of what the module does&lt;br /&gt;
description This is an example of an extension module written in python&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9498</id>
		<title>Slicer3:Extensions</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9498"/>
		<updated>2009-05-08T21:29:34Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* FOR DEVELOPERS */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;3D Slicer now supports extensions.  Extensions are available from an extension server.  This allows end-users to select the extensions useful to them, without having to download the entire extension archive.&lt;br /&gt;
&lt;br /&gt;
== FOR DEVELOPERS ==&lt;br /&gt;
&lt;br /&gt;
Extensions must follow the appropriate architecture for them to be made available to end users.  See [[Slicer3::Loadable_Modules]] for an example of how to make GUI and GUI-less Loadable Modules.  Command Line and Scripted Modules will also work with this framework.&lt;br /&gt;
&lt;br /&gt;
To enable your Command Line, Scripted, or Loadable module, add an &amp;quot;s3ext&amp;quot; script to the /Slicer3/Extensions directory of the source repository:&lt;br /&gt;
&lt;br /&gt;
PythonSampleScriptedModule.s3ext:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
#&lt;br /&gt;
# first token of each non-comment line is the keyword and the rest of the line &lt;br /&gt;
# (including spaces) is the value.&lt;br /&gt;
# - the value can be blank&lt;br /&gt;
#&lt;br /&gt;
&lt;br /&gt;
# scm is source code manager (i.e. svn)&lt;br /&gt;
scm       svn&lt;br /&gt;
svnpath   https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules/Scripted/PythonSampleScriptedModule&lt;br /&gt;
svnusername slicerbot&lt;br /&gt;
svnpassword slicer&lt;br /&gt;
&lt;br /&gt;
# list dependencies &lt;br /&gt;
# - these should be names of other modules that have .s3ext files &lt;br /&gt;
# - the dependencies will be built first&lt;br /&gt;
depends ScriptedModule&lt;br /&gt;
&lt;br /&gt;
# homepage&lt;br /&gt;
homepage  http://www.slicer.org&lt;br /&gt;
&lt;br /&gt;
# match category in the xml description of the module (where it shows up in Modules menu)&lt;br /&gt;
category  Developer Tools&lt;br /&gt;
&lt;br /&gt;
# give people an idea what to expect from this code &lt;br /&gt;
# - is it just a test or something you stand beind?&lt;br /&gt;
status    Beta&lt;br /&gt;
&lt;br /&gt;
# One line description of what the module does&lt;br /&gt;
description This is an example of an extension module written in python&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9497</id>
		<title>Documentation/3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9497"/>
		<updated>2009-05-08T21:17:53Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Main GUI */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Note: This page is currently under construction&lt;br /&gt;
&lt;br /&gt;
=Introduction=&lt;br /&gt;
[[Image:Base-Features-and-Modules.png|thumb|right|overview|[[Media:Integrating with Slicer3.ppt | Integrating with Slicer3]]]]&lt;br /&gt;
This page is a portal for documentation about Slicer 3.4.&lt;br /&gt;
For information for software developers, please go to the Developers page (see link in navigation box to the left).&lt;br /&gt;
&lt;br /&gt;
=How-To Tutorials=&lt;br /&gt;
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]&lt;br /&gt;
&lt;br /&gt;
=Feature Request and Problem Reports=&lt;br /&gt;
We have an [http://www.na-mic.org/Bug/my_view_page.php issues tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.&lt;br /&gt;
&lt;br /&gt;
=List of Modules=&lt;br /&gt;
==Overview==&lt;br /&gt;
*The documentation on this page has been created for Slicer 3.4 and discusses the features and capabilities of menu items and panels. It is intended to be used as a live reference manual. This is a wiki. You are welcome to add to the content and improve it.&lt;br /&gt;
*In addition to the hundereds of smaller changes and improvements to Slicer in general, there are two substantial new addtions to Slicer 3.4:&lt;br /&gt;
**A new infrastructure to find and add plug-ins from a repository. See [[Documentation-3.4#Modules_for_Downloading|here]] for more information.&lt;br /&gt;
**A new database using XNAT desktop. See [[Documentation-3.4#XNAT_Desktop|here]] for more information.&lt;br /&gt;
&lt;br /&gt;
==Main GUI==&lt;br /&gt;
*[[Modules:MainApplicationGUI-Documentation-3.4| Main Application GUI]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:EventBindings-3.4| &amp;quot;Hot-keys&amp;quot; and Keyboard Shortcuts]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:DataModule-3.4| Loading Scenes and Individual Datasets through the Data Module]] (W Plesniak)&lt;br /&gt;
*[[Modules:Loading-Data-3.4| Data Loading Details]] (Steve Pieper)&lt;br /&gt;
*[[Modules:Saving-Documentation-3.4| Saving Scenes and Data]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:SceneSnapshots-3.4| Creating and Restoring Scene Snapshots]] (Alex Yarmarkovich &amp;amp; Steve Pieper)&lt;br /&gt;
*[[Modules:ExtensionsManagementWizard-Documentation-3.4| Extensions Management Wizard]] (Terry Lorber)&lt;br /&gt;
&lt;br /&gt;
==Modules==&lt;br /&gt;
*Please copy the template linked below, paste it into your page and customize it with your module's information.&lt;br /&gt;
[[Slicer3:Module_Documentation-3.4_Template|Slicer3:Module_Documentation-3.4_Template]]&lt;br /&gt;
*See above for info to be put into the Help and Acknowledgment Tabs&lt;br /&gt;
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]&lt;br /&gt;
===Core===&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)&lt;br /&gt;
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)&lt;br /&gt;
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]]  (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)&lt;br /&gt;
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)&lt;br /&gt;
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)&lt;br /&gt;
&lt;br /&gt;
Additional modules may appear in this section of the menu if they are not otherwise categorized by the developer.&lt;br /&gt;
&lt;br /&gt;
==Specialized Modules==&lt;br /&gt;
&lt;br /&gt;
Please adhere to the naming scheme for the module documentation:&lt;br /&gt;
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)&lt;br /&gt;
&lt;br /&gt;
===Wizards===&lt;br /&gt;
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)&lt;br /&gt;
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)&lt;br /&gt;
===Informatics Modules===&lt;br /&gt;
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)&lt;br /&gt;
===Registration===&lt;br /&gt;
*Overview:&lt;br /&gt;
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies. &lt;br /&gt;
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment. &lt;br /&gt;
**Linear, affine  and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output. &lt;br /&gt;
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.&lt;br /&gt;
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)&lt;br /&gt;
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)&lt;br /&gt;
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]]  (Daniel Blezek)&lt;br /&gt;
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Segmentation===&lt;br /&gt;
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)&lt;br /&gt;
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
===Statistics===&lt;br /&gt;
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Diffusion===&lt;br /&gt;
====DWI====&lt;br /&gt;
*Estimation&lt;br /&gt;
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
*Filter&lt;br /&gt;
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)&lt;br /&gt;
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)&lt;br /&gt;
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
====DTI====&lt;br /&gt;
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)&lt;br /&gt;
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)&lt;br /&gt;
*Analysis&lt;br /&gt;
&lt;br /&gt;
===Tractography===&lt;br /&gt;
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)&lt;br /&gt;
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)&lt;br /&gt;
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
===IGT===&lt;br /&gt;
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) &lt;br /&gt;
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)&lt;br /&gt;
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)&lt;br /&gt;
===Filtering===&lt;br /&gt;
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)&lt;br /&gt;
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)&lt;br /&gt;
*Arithmetic&lt;br /&gt;
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)&lt;br /&gt;
*Denoising&lt;br /&gt;
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]]  (Bill Lorensen checked this in)&lt;br /&gt;
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) &lt;br /&gt;
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)&lt;br /&gt;
*Morphology&lt;br /&gt;
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)&lt;br /&gt;
===Surface Models===&lt;br /&gt;
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)&lt;br /&gt;
*Grayscale Model Maker (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
*Freesurfer Surface Section Extraction (Katharina Quintus)&lt;br /&gt;
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Batch processing===&lt;br /&gt;
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)&lt;br /&gt;
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)&lt;br /&gt;
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)&lt;br /&gt;
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)&lt;br /&gt;
&lt;br /&gt;
===Converters===&lt;br /&gt;
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)&lt;br /&gt;
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Work in Progress===&lt;br /&gt;
Various tools in development will appear here depending on the version of slicer you are using.&lt;br /&gt;
===Developer Tools===&lt;br /&gt;
*[[Modules:PythonScript-Documentation-3.4| Python Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonNumpyScript-Documentation-3.4| Python Numpy Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExecutionModelTour-Documentation-3.4|Execution Model Tour]] (Daniel Blezek, Bill Lorensen)&lt;br /&gt;
*[[Modules:ScriptedModuleExample-Documentation-3.4| Scripted Module Example]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
=Extensions for Downloading=&lt;br /&gt;
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]&lt;br /&gt;
Work is in progress to create infrastructure for searching and loading extensions. See [[Slicer3:Extensions]] for more information.&lt;br /&gt;
*This will allow contributors and software developers to post their own Slicer extensions and have them compiled against the &amp;quot;official&amp;quot; versions of Slicer.&lt;br /&gt;
*Users can browse these contributed extensions and install them on their own versions of Slicer.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
We are currently using NITRC as a repository for contributed extensions. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.&lt;br /&gt;
Click [http://www.nitrc.org/search/?type_of_search=soft&amp;amp;words=slicer3&amp;amp;Search.x=0&amp;amp;Search.y=0&amp;amp;Search=Search  here] to see a listing of Slicer 3 extensions on NITRC.&lt;br /&gt;
&lt;br /&gt;
=XNAT Desktop and FetchMI=&lt;br /&gt;
*Work is underway to use XNAT desktop (xnd) as a local database for Slicer. This database will exist in parallel with the other load and save mechanisms and will allow to download/upload individual files or entire scenes with all their dependent files. &lt;br /&gt;
*Users of Slicer will have to install xnd on their computer. Once set up, the FetchMI interface will allow users to upload and download mrml scenes with all the dependent files, or individual volumes, models, other components of slicer scenes.&lt;br /&gt;
*See [http://nrg.wustl.edu/xnd/download here] for a link to the download site for xnd. See [http://www.xnat.org/xnd here] for documentation on how to install XNAT desktop on your computer.&lt;br /&gt;
*'''On Macs and Linux you currently have to change permissions of the executable after installation.'''&lt;br /&gt;
*In the future (summer 2009) xnd will be able to upload and download mrml scenes to xnat enterprise.&lt;br /&gt;
&lt;br /&gt;
*FetchMI is the current interface inside slicer for exploring information stored in xnd and down and upload such data. It is a &amp;quot;sandbox&amp;quot; implementation to help us understand how users will want to use remotely stored data and metadata in the Slicer environment. Eventually, FetchMI's remote load and save will be integrated with Slicer's existing load and save interfaces, and FetchMI's data tagging functionality will be more fully developed as a new metadata authoring module.&lt;br /&gt;
*See [[Modules:FetchMI-Documentation-3.4|here]] for more information about FETCHMI. User comments and suggestions are welcome.&lt;br /&gt;
&lt;br /&gt;
= Requirements for modules to be added to the release=&lt;br /&gt;
{| border=&amp;quot;00&amp;quot; cellpadding=&amp;quot;5&amp;quot; cellspacing=&amp;quot;0&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
| rowspan=&amp;quot;2&amp;quot;| &lt;br /&gt;
* The module is '''feature complete''' for the tasks advertised on 2-4-2009&lt;br /&gt;
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.&lt;br /&gt;
* Module has '''documentation''' on the [[Documentation-3.4#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.4#Modules|'''here''']] to structure your page. &lt;br /&gt;
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.&lt;br /&gt;
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.&lt;br /&gt;
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.&lt;br /&gt;
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. &lt;br /&gt;
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)&lt;br /&gt;
* If your module has [[Documentation-3.2|documentation in Slicer 3.2]], please copy/paste/update into the 3.4 version&lt;br /&gt;
| style=&amp;quot;background: #e5e5e5&amp;quot; align=&amp;quot;center&amp;quot;| Examples for the Help and &lt;br /&gt;
Acknowledgment Panels&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background: #ebeced&amp;quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] &lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9496</id>
		<title>Documentation/3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9496"/>
		<updated>2009-05-08T21:16:53Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Main GUI */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Note: This page is currently under construction&lt;br /&gt;
&lt;br /&gt;
=Introduction=&lt;br /&gt;
[[Image:Base-Features-and-Modules.png|thumb|right|overview|[[Media:Integrating with Slicer3.ppt | Integrating with Slicer3]]]]&lt;br /&gt;
This page is a portal for documentation about Slicer 3.4.&lt;br /&gt;
For information for software developers, please go to the Developers page (see link in navigation box to the left).&lt;br /&gt;
&lt;br /&gt;
=How-To Tutorials=&lt;br /&gt;
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]&lt;br /&gt;
&lt;br /&gt;
=Feature Request and Problem Reports=&lt;br /&gt;
We have an [http://www.na-mic.org/Bug/my_view_page.php issues tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.&lt;br /&gt;
&lt;br /&gt;
=List of Modules=&lt;br /&gt;
==Overview==&lt;br /&gt;
*The documentation on this page has been created for Slicer 3.4 and discusses the features and capabilities of menu items and panels. It is intended to be used as a live reference manual. This is a wiki. You are welcome to add to the content and improve it.&lt;br /&gt;
*In addition to the hundereds of smaller changes and improvements to Slicer in general, there are two substantial new addtions to Slicer 3.4:&lt;br /&gt;
**A new infrastructure to find and add plug-ins from a repository. See [[Documentation-3.4#Modules_for_Downloading|here]] for more information.&lt;br /&gt;
**A new database using XNAT desktop. See [[Documentation-3.4#XNAT_Desktop|here]] for more information.&lt;br /&gt;
&lt;br /&gt;
==Main GUI==&lt;br /&gt;
*[[Modules:MainApplicationGUI-Documentation-3.4| Main Application GUI]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:EventBindings-3.4| &amp;quot;Hot-keys&amp;quot; and Keyboard Shortcuts]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:DataModule-3.4| Loading Scenes and Individual Datasets through the Data Module]] (W Plesniak)&lt;br /&gt;
*[[Modules:Loading-Data-3.4| Data Loading Details]] (Steve Pieper)&lt;br /&gt;
*[[Modules:Saving-Documentation-3.4| Saving Scenes and Data]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:SceneSnapshots-3.4| Creating and Restoring Scene Snapshots]] (Alex Yarmarkovich &amp;amp; Steve Pieper)&lt;br /&gt;
*[[Modules:ExtensionsManagementWizard-3.4| Extensions Management Wizard]] (Terry Lorber)&lt;br /&gt;
&lt;br /&gt;
==Modules==&lt;br /&gt;
*Please copy the template linked below, paste it into your page and customize it with your module's information.&lt;br /&gt;
[[Slicer3:Module_Documentation-3.4_Template|Slicer3:Module_Documentation-3.4_Template]]&lt;br /&gt;
*See above for info to be put into the Help and Acknowledgment Tabs&lt;br /&gt;
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]&lt;br /&gt;
===Core===&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)&lt;br /&gt;
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)&lt;br /&gt;
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]]  (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)&lt;br /&gt;
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)&lt;br /&gt;
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)&lt;br /&gt;
&lt;br /&gt;
Additional modules may appear in this section of the menu if they are not otherwise categorized by the developer.&lt;br /&gt;
&lt;br /&gt;
==Specialized Modules==&lt;br /&gt;
&lt;br /&gt;
Please adhere to the naming scheme for the module documentation:&lt;br /&gt;
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)&lt;br /&gt;
&lt;br /&gt;
===Wizards===&lt;br /&gt;
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)&lt;br /&gt;
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)&lt;br /&gt;
===Informatics Modules===&lt;br /&gt;
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)&lt;br /&gt;
===Registration===&lt;br /&gt;
*Overview:&lt;br /&gt;
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies. &lt;br /&gt;
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment. &lt;br /&gt;
**Linear, affine  and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output. &lt;br /&gt;
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.&lt;br /&gt;
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)&lt;br /&gt;
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)&lt;br /&gt;
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]]  (Daniel Blezek)&lt;br /&gt;
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Segmentation===&lt;br /&gt;
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)&lt;br /&gt;
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
===Statistics===&lt;br /&gt;
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Diffusion===&lt;br /&gt;
====DWI====&lt;br /&gt;
*Estimation&lt;br /&gt;
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
*Filter&lt;br /&gt;
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)&lt;br /&gt;
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)&lt;br /&gt;
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
====DTI====&lt;br /&gt;
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)&lt;br /&gt;
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)&lt;br /&gt;
*Analysis&lt;br /&gt;
&lt;br /&gt;
===Tractography===&lt;br /&gt;
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)&lt;br /&gt;
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)&lt;br /&gt;
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
===IGT===&lt;br /&gt;
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) &lt;br /&gt;
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)&lt;br /&gt;
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)&lt;br /&gt;
===Filtering===&lt;br /&gt;
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)&lt;br /&gt;
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)&lt;br /&gt;
*Arithmetic&lt;br /&gt;
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)&lt;br /&gt;
*Denoising&lt;br /&gt;
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]]  (Bill Lorensen checked this in)&lt;br /&gt;
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) &lt;br /&gt;
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)&lt;br /&gt;
*Morphology&lt;br /&gt;
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)&lt;br /&gt;
===Surface Models===&lt;br /&gt;
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)&lt;br /&gt;
*Grayscale Model Maker (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
*Freesurfer Surface Section Extraction (Katharina Quintus)&lt;br /&gt;
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Batch processing===&lt;br /&gt;
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)&lt;br /&gt;
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)&lt;br /&gt;
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)&lt;br /&gt;
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)&lt;br /&gt;
&lt;br /&gt;
===Converters===&lt;br /&gt;
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)&lt;br /&gt;
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Work in Progress===&lt;br /&gt;
Various tools in development will appear here depending on the version of slicer you are using.&lt;br /&gt;
===Developer Tools===&lt;br /&gt;
*[[Modules:PythonScript-Documentation-3.4| Python Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonNumpyScript-Documentation-3.4| Python Numpy Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExecutionModelTour-Documentation-3.4|Execution Model Tour]] (Daniel Blezek, Bill Lorensen)&lt;br /&gt;
*[[Modules:ScriptedModuleExample-Documentation-3.4| Scripted Module Example]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
=Extensions for Downloading=&lt;br /&gt;
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]&lt;br /&gt;
Work is in progress to create infrastructure for searching and loading extensions. See [[Slicer3:Extensions]] for more information.&lt;br /&gt;
*This will allow contributors and software developers to post their own Slicer extensions and have them compiled against the &amp;quot;official&amp;quot; versions of Slicer.&lt;br /&gt;
*Users can browse these contributed extensions and install them on their own versions of Slicer.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
We are currently using NITRC as a repository for contributed extensions. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.&lt;br /&gt;
Click [http://www.nitrc.org/search/?type_of_search=soft&amp;amp;words=slicer3&amp;amp;Search.x=0&amp;amp;Search.y=0&amp;amp;Search=Search  here] to see a listing of Slicer 3 extensions on NITRC.&lt;br /&gt;
&lt;br /&gt;
=XNAT Desktop and FetchMI=&lt;br /&gt;
*Work is underway to use XNAT desktop (xnd) as a local database for Slicer. This database will exist in parallel with the other load and save mechanisms and will allow to download/upload individual files or entire scenes with all their dependent files. &lt;br /&gt;
*Users of Slicer will have to install xnd on their computer. Once set up, the FetchMI interface will allow users to upload and download mrml scenes with all the dependent files, or individual volumes, models, other components of slicer scenes.&lt;br /&gt;
*See [http://nrg.wustl.edu/xnd/download here] for a link to the download site for xnd. See [http://www.xnat.org/xnd here] for documentation on how to install XNAT desktop on your computer.&lt;br /&gt;
*'''On Macs and Linux you currently have to change permissions of the executable after installation.'''&lt;br /&gt;
*In the future (summer 2009) xnd will be able to upload and download mrml scenes to xnat enterprise.&lt;br /&gt;
&lt;br /&gt;
*FetchMI is the current interface inside slicer for exploring information stored in xnd and down and upload such data. It is a &amp;quot;sandbox&amp;quot; implementation to help us understand how users will want to use remotely stored data and metadata in the Slicer environment. Eventually, FetchMI's remote load and save will be integrated with Slicer's existing load and save interfaces, and FetchMI's data tagging functionality will be more fully developed as a new metadata authoring module.&lt;br /&gt;
*See [[Modules:FetchMI-Documentation-3.4|here]] for more information about FETCHMI. User comments and suggestions are welcome.&lt;br /&gt;
&lt;br /&gt;
= Requirements for modules to be added to the release=&lt;br /&gt;
{| border=&amp;quot;00&amp;quot; cellpadding=&amp;quot;5&amp;quot; cellspacing=&amp;quot;0&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
| rowspan=&amp;quot;2&amp;quot;| &lt;br /&gt;
* The module is '''feature complete''' for the tasks advertised on 2-4-2009&lt;br /&gt;
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.&lt;br /&gt;
* Module has '''documentation''' on the [[Documentation-3.4#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.4#Modules|'''here''']] to structure your page. &lt;br /&gt;
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.&lt;br /&gt;
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.&lt;br /&gt;
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.&lt;br /&gt;
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. &lt;br /&gt;
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)&lt;br /&gt;
* If your module has [[Documentation-3.2|documentation in Slicer 3.2]], please copy/paste/update into the 3.4 version&lt;br /&gt;
| style=&amp;quot;background: #e5e5e5&amp;quot; align=&amp;quot;center&amp;quot;| Examples for the Help and &lt;br /&gt;
Acknowledgment Panels&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background: #ebeced&amp;quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] &lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9495</id>
		<title>Documentation/3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9495"/>
		<updated>2009-05-08T21:16:37Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Main GUI */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Note: This page is currently under construction&lt;br /&gt;
&lt;br /&gt;
=Introduction=&lt;br /&gt;
[[Image:Base-Features-and-Modules.png|thumb|right|overview|[[Media:Integrating with Slicer3.ppt | Integrating with Slicer3]]]]&lt;br /&gt;
This page is a portal for documentation about Slicer 3.4.&lt;br /&gt;
For information for software developers, please go to the Developers page (see link in navigation box to the left).&lt;br /&gt;
&lt;br /&gt;
=How-To Tutorials=&lt;br /&gt;
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]&lt;br /&gt;
&lt;br /&gt;
=Feature Request and Problem Reports=&lt;br /&gt;
We have an [http://www.na-mic.org/Bug/my_view_page.php issues tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.&lt;br /&gt;
&lt;br /&gt;
=List of Modules=&lt;br /&gt;
==Overview==&lt;br /&gt;
*The documentation on this page has been created for Slicer 3.4 and discusses the features and capabilities of menu items and panels. It is intended to be used as a live reference manual. This is a wiki. You are welcome to add to the content and improve it.&lt;br /&gt;
*In addition to the hundereds of smaller changes and improvements to Slicer in general, there are two substantial new addtions to Slicer 3.4:&lt;br /&gt;
**A new infrastructure to find and add plug-ins from a repository. See [[Documentation-3.4#Modules_for_Downloading|here]] for more information.&lt;br /&gt;
**A new database using XNAT desktop. See [[Documentation-3.4#XNAT_Desktop|here]] for more information.&lt;br /&gt;
&lt;br /&gt;
==Main GUI==&lt;br /&gt;
*[[Modules:MainApplicationGUI-Documentation-3.4| Main Application GUI]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:EventBindings-3.4| &amp;quot;Hot-keys&amp;quot; and Keyboard Shortcuts]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:DataModule-3.4| Loading Scenes and Individual Datasets through the Data Module]] (W Plesniak)&lt;br /&gt;
*[[Modules:Loading-Data-3.4| Data Loading Details]] (Steve Pieper)&lt;br /&gt;
*[[Modules:Saving-Documentation-3.4| Saving Scenes and Data]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:SceneSnapshots-3.4| Creating and Restoring Scene Snapshots]] (Alex Yarmarkovich &amp;amp; Steve Pieper)&lt;br /&gt;
*[[Modules:ExtensionsManagementWizard| Extensions Management Wizard]](Terry Lorber)&lt;br /&gt;
&lt;br /&gt;
==Modules==&lt;br /&gt;
*Please copy the template linked below, paste it into your page and customize it with your module's information.&lt;br /&gt;
[[Slicer3:Module_Documentation-3.4_Template|Slicer3:Module_Documentation-3.4_Template]]&lt;br /&gt;
*See above for info to be put into the Help and Acknowledgment Tabs&lt;br /&gt;
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]&lt;br /&gt;
===Core===&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)&lt;br /&gt;
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)&lt;br /&gt;
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]]  (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)&lt;br /&gt;
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)&lt;br /&gt;
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)&lt;br /&gt;
&lt;br /&gt;
Additional modules may appear in this section of the menu if they are not otherwise categorized by the developer.&lt;br /&gt;
&lt;br /&gt;
==Specialized Modules==&lt;br /&gt;
&lt;br /&gt;
Please adhere to the naming scheme for the module documentation:&lt;br /&gt;
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)&lt;br /&gt;
&lt;br /&gt;
===Wizards===&lt;br /&gt;
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)&lt;br /&gt;
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)&lt;br /&gt;
===Informatics Modules===&lt;br /&gt;
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)&lt;br /&gt;
===Registration===&lt;br /&gt;
*Overview:&lt;br /&gt;
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies. &lt;br /&gt;
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment. &lt;br /&gt;
**Linear, affine  and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output. &lt;br /&gt;
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.&lt;br /&gt;
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)&lt;br /&gt;
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)&lt;br /&gt;
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]]  (Daniel Blezek)&lt;br /&gt;
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Segmentation===&lt;br /&gt;
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)&lt;br /&gt;
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
===Statistics===&lt;br /&gt;
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Diffusion===&lt;br /&gt;
====DWI====&lt;br /&gt;
*Estimation&lt;br /&gt;
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
*Filter&lt;br /&gt;
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)&lt;br /&gt;
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)&lt;br /&gt;
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
====DTI====&lt;br /&gt;
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)&lt;br /&gt;
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)&lt;br /&gt;
*Analysis&lt;br /&gt;
&lt;br /&gt;
===Tractography===&lt;br /&gt;
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)&lt;br /&gt;
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)&lt;br /&gt;
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
===IGT===&lt;br /&gt;
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) &lt;br /&gt;
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)&lt;br /&gt;
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)&lt;br /&gt;
===Filtering===&lt;br /&gt;
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)&lt;br /&gt;
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)&lt;br /&gt;
*Arithmetic&lt;br /&gt;
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)&lt;br /&gt;
*Denoising&lt;br /&gt;
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]]  (Bill Lorensen checked this in)&lt;br /&gt;
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) &lt;br /&gt;
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)&lt;br /&gt;
*Morphology&lt;br /&gt;
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)&lt;br /&gt;
===Surface Models===&lt;br /&gt;
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)&lt;br /&gt;
*Grayscale Model Maker (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
*Freesurfer Surface Section Extraction (Katharina Quintus)&lt;br /&gt;
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Batch processing===&lt;br /&gt;
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)&lt;br /&gt;
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)&lt;br /&gt;
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)&lt;br /&gt;
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)&lt;br /&gt;
&lt;br /&gt;
===Converters===&lt;br /&gt;
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)&lt;br /&gt;
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Work in Progress===&lt;br /&gt;
Various tools in development will appear here depending on the version of slicer you are using.&lt;br /&gt;
===Developer Tools===&lt;br /&gt;
*[[Modules:PythonScript-Documentation-3.4| Python Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonNumpyScript-Documentation-3.4| Python Numpy Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExecutionModelTour-Documentation-3.4|Execution Model Tour]] (Daniel Blezek, Bill Lorensen)&lt;br /&gt;
*[[Modules:ScriptedModuleExample-Documentation-3.4| Scripted Module Example]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
=Extensions for Downloading=&lt;br /&gt;
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]&lt;br /&gt;
Work is in progress to create infrastructure for searching and loading extensions. See [[Slicer3:Extensions]] for more information.&lt;br /&gt;
*This will allow contributors and software developers to post their own Slicer extensions and have them compiled against the &amp;quot;official&amp;quot; versions of Slicer.&lt;br /&gt;
*Users can browse these contributed extensions and install them on their own versions of Slicer.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
We are currently using NITRC as a repository for contributed extensions. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.&lt;br /&gt;
Click [http://www.nitrc.org/search/?type_of_search=soft&amp;amp;words=slicer3&amp;amp;Search.x=0&amp;amp;Search.y=0&amp;amp;Search=Search  here] to see a listing of Slicer 3 extensions on NITRC.&lt;br /&gt;
&lt;br /&gt;
=XNAT Desktop and FetchMI=&lt;br /&gt;
*Work is underway to use XNAT desktop (xnd) as a local database for Slicer. This database will exist in parallel with the other load and save mechanisms and will allow to download/upload individual files or entire scenes with all their dependent files. &lt;br /&gt;
*Users of Slicer will have to install xnd on their computer. Once set up, the FetchMI interface will allow users to upload and download mrml scenes with all the dependent files, or individual volumes, models, other components of slicer scenes.&lt;br /&gt;
*See [http://nrg.wustl.edu/xnd/download here] for a link to the download site for xnd. See [http://www.xnat.org/xnd here] for documentation on how to install XNAT desktop on your computer.&lt;br /&gt;
*'''On Macs and Linux you currently have to change permissions of the executable after installation.'''&lt;br /&gt;
*In the future (summer 2009) xnd will be able to upload and download mrml scenes to xnat enterprise.&lt;br /&gt;
&lt;br /&gt;
*FetchMI is the current interface inside slicer for exploring information stored in xnd and down and upload such data. It is a &amp;quot;sandbox&amp;quot; implementation to help us understand how users will want to use remotely stored data and metadata in the Slicer environment. Eventually, FetchMI's remote load and save will be integrated with Slicer's existing load and save interfaces, and FetchMI's data tagging functionality will be more fully developed as a new metadata authoring module.&lt;br /&gt;
*See [[Modules:FetchMI-Documentation-3.4|here]] for more information about FETCHMI. User comments and suggestions are welcome.&lt;br /&gt;
&lt;br /&gt;
= Requirements for modules to be added to the release=&lt;br /&gt;
{| border=&amp;quot;00&amp;quot; cellpadding=&amp;quot;5&amp;quot; cellspacing=&amp;quot;0&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
| rowspan=&amp;quot;2&amp;quot;| &lt;br /&gt;
* The module is '''feature complete''' for the tasks advertised on 2-4-2009&lt;br /&gt;
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.&lt;br /&gt;
* Module has '''documentation''' on the [[Documentation-3.4#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.4#Modules|'''here''']] to structure your page. &lt;br /&gt;
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.&lt;br /&gt;
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.&lt;br /&gt;
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.&lt;br /&gt;
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. &lt;br /&gt;
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)&lt;br /&gt;
* If your module has [[Documentation-3.2|documentation in Slicer 3.2]], please copy/paste/update into the 3.4 version&lt;br /&gt;
| style=&amp;quot;background: #e5e5e5&amp;quot; align=&amp;quot;center&amp;quot;| Examples for the Help and &lt;br /&gt;
Acknowledgment Panels&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background: #ebeced&amp;quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] &lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Modules:ExtensionsManagementWizard-Documentation-3.4&amp;diff=9494</id>
		<title>Modules:ExtensionsManagementWizard-Documentation-3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Modules:ExtensionsManagementWizard-Documentation-3.4&amp;diff=9494"/>
		<updated>2009-05-08T21:15:42Z</updated>

		<summary type="html">&lt;p&gt;Tgl: New page: Placeholder for description of the Extensions Management Wizard in 3.4&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Placeholder for description of the Extensions Management Wizard in 3.4&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Modules:MainApplicationGUI-Documentation-3.4&amp;diff=9493</id>
		<title>Modules:MainApplicationGUI-Documentation-3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Modules:MainApplicationGUI-Documentation-3.4&amp;diff=9493"/>
		<updated>2009-05-08T21:15:19Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* View menu */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[Documentation-3.4#Main_GUI|Return to Slicer Documentation]]&lt;br /&gt;
&lt;br /&gt;
'''Overview'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Slicer3's main desktop interface provides top-level access to most commonly-used features, and organizes them into logical groupings. These groups of features are presented in a number of interface panels on the GUI, as is illustrated in the basic layout below. The interface is designed to be easy to learn and remember, to ease navigation of Slicer's large (and growing) functionality, and to easily collapse and hide when you don't need to see it. Figures A through I in the &amp;quot;Individual frames&amp;quot; gallery a little further down on this page provide richer detail and will be described in the following sections.&lt;br /&gt;
&lt;br /&gt;
[[image:SlicerGUIIntro.png ]]&lt;br /&gt;
&lt;br /&gt;
As shown above, the logical groupings of Slicer's interface elements include:&lt;br /&gt;
* The Application Menubar&lt;br /&gt;
* The Application Toolbar&lt;br /&gt;
* The Main GUI Panel, which consists of:&lt;br /&gt;
** Slicer's Logo Panel&lt;br /&gt;
** The Module GUI Panel&lt;br /&gt;
** The Slice Viewer Controls&lt;br /&gt;
** The 3D Viewer Controls&lt;br /&gt;
* The 3D Viewer&lt;br /&gt;
* Three Main Slice Viewers (Red, Yellow, and Green)and additional Slice Viewers&lt;br /&gt;
* The Message Bar and Progress Gauge&lt;br /&gt;
* And the Error Log Button&lt;br /&gt;
&lt;br /&gt;
An overview of the functionality provided in each of these interface elements is provided below.&lt;br /&gt;
&lt;br /&gt;
=Individual Panels=&lt;br /&gt;
&lt;br /&gt;
&amp;lt;gallery perrow=&amp;quot;3&amp;quot; widths=&amp;quot;300px&amp;quot; heights=&amp;quot;200px&amp;quot;&amp;gt;&lt;br /&gt;
Image:AppGUIMap.png | '''Figure A.''' Schematic of the [[ Modules:MainApplicationGUI-Documentation-3.2#Main_Application_GUI_organization | main application GUI ]]&lt;br /&gt;
Image:AppToolbarMap.png | '''Figure B.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#Application_Toolbar | Application Toolbar ]]&lt;br /&gt;
Image:SCGUIMap.png | '''Figure C.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewer_Control_Panel | Controller for all Slice Viewers ]]&lt;br /&gt;
Image:VCGUIMap.png | '''Figure D.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#3D_Viewer_Control_Panel | Controller for the 3D Viewer ]]&lt;br /&gt;
image:SliceGUIMap.png | '''Figure E.''' Schematic of a [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewers_.26_Controllers | Slice Viewer and Slice Controller]]&lt;br /&gt;
Image:ModuleGUIPanel.png | '''Figure F.''' Schematic of an [[Modules:MainApplicationGUI-Documentation-3.4#Module_GUI_Panel | expanding/collapsing module GUI panel ]]&lt;br /&gt;
Image:SliceGUIMoreMap.png | '''Figure G.''' Schematic of [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewers_.26_Controllers | Slice Viewer additional options ]]&lt;br /&gt;
Image:AppSettingsGUIMap.png | '''Figure H.''' Schematics of the [[Modules:MainApplicationGUI-Documentation-3.2#View-.3EApplication_Settings_Interface: | Application Settings Interface ]]&lt;br /&gt;
Image:RemoteIOGUIMap.png | '''Figure I.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#View-.3ECache_.26_RemoteIO_Manager: | Remote Data Handling Interface ]]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Application Menubar =&lt;br /&gt;
The Application menubar is at the very top of Slicer3's main window, as noted above and in Figure A. Its menus and functionality are briefly listed below.&lt;br /&gt;
&lt;br /&gt;
== File menu ==&lt;br /&gt;
&lt;br /&gt;
Several loading options are available from the file menu. Below is a '''general overview''' of these options. For more details and suggestions for common use cases, see [[ Modules:Loading-Data-3.4 | Data loading details for Slicer3.4]]. For information about accessing the functionality described below and loading other types of data (like transforms, fiducial lists, color tables, DTI fiber bundles ''etc''.) through the Data Module, see [[Modules:DataModule-3.4 | Slicer's Data Module documentation]].&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Load Scene:''' &lt;br /&gt;
&lt;br /&gt;
This command raises a file browser (shown below). Slicer's file browser has a 'favorites' icon that allows you to save often-visited directories on the browser's left panel. Other features, including icons that allow you to navigate your browsing history, pop up a level in the directory structure (or folder hierarchy) and create new folders. To load a scene, navigate to a file of the appropriate format (.mrml, .xcat (XCEDE catalog file), or .xml (Slicer2 scene file) and select it for loading into Slicer. '''The command first clears any existing scene''' in Slicer and '''resets the application state'''.&lt;br /&gt;
&lt;br /&gt;
[[image:FileBrowser.png]]&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Import Scene:'''&lt;br /&gt;
&lt;br /&gt;
This command raises the same file browser shown above. Navigate to and select a scene file to be added to the existing Slicer scene. '''(The existing scene is not cleared)'''.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Add Data:'''&lt;br /&gt;
&lt;br /&gt;
This command raises an &amp;quot;Add Data&amp;quot; widget (shown below) that allows you to select individual datasets to add to the existing scene. This load option is most useful when you want to load many different data types at once (volumes, models, ''etc.'') which may not yet be described by a scene file. It exposes the following functionality:&lt;br /&gt;
&lt;br /&gt;
* The &amp;quot;Add Directory&amp;quot; button adds all files within the selected directory to the file list.&lt;br /&gt;
* The &amp;quot;Add File(s)&amp;quot; button adds all selected files to the file list.&lt;br /&gt;
* The array of buttons across the top allow you to select and deselect files in the file list, remove selected files from the list, or describe how files should be loaded.&lt;br /&gt;
* The &amp;quot;Apply&amp;quot; button loads all datasets in the list, and&lt;br /&gt;
* The &amp;quot;Cancel&amp;quot; button aborts the entire load.&lt;br /&gt;
&lt;br /&gt;
[[image:AppAddData.png]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Add Volume:''' &lt;br /&gt;
&lt;br /&gt;
This command raises an &amp;quot;Add Volume&amp;quot; widget (shown below) that allows you to select a volumetric dataset to add to the existing scene. The &amp;quot;Volume Options&amp;quot; panel can be used to clarify how a selected dataset should be loaded and displayed. This load option is particularly useful for loading DICOM data, for which its DICOM information parsing panel can be helpful.&lt;br /&gt;
&lt;br /&gt;
[[image:AppAddVolume.png]]&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Save:'''&lt;br /&gt;
&lt;br /&gt;
This command displays the &amp;quot;Save Data&amp;quot; widget, which offers many options for saving a scene and/or individual datasets. The widget is shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppSaveData.png]]&lt;br /&gt;
&lt;br /&gt;
'''Specifying a scene file to save:''' The ''Scene Description'' entry is always listed in the top row of the table. If a scene has already been loaded from a MRML file, then its filename is presented as the default choice. To save the scene into a '''new''' MRML file, either provide an alternate file name, or provide a new Data Directory.  &lt;br /&gt;
&lt;br /&gt;
'''Indicating new and unsaved datasets:''' When the panel is first displayed, all datasets which have been newly created or modified since the scene was saved are checked by default in the ''Save'' column. Any datasets in the scene can be checked/unchecked for saving/not saving using the checkboxes provided in this column. The icon buttons in the top left corner (from left to right) of the window provide shortcuts to modify the default selection:&lt;br /&gt;
&lt;br /&gt;
* '''Select Scene and Modified Data''', &lt;br /&gt;
* '''Select Modified Data'''only,&lt;br /&gt;
* '''Select All''', and&lt;br /&gt;
* '''Select None'''.&lt;br /&gt;
&lt;br /&gt;
These icons are shown and annotated below, under the SaveData illustration. Any individual checkbox can also be used to modify the selection state.  &lt;br /&gt;
&lt;br /&gt;
[[image:AppSaveDataIcons.png]]&lt;br /&gt;
&lt;br /&gt;
'''Converting to other data formats:''' Any dataset can be converted to a different (supported) format by editing the filename extension. '''Note that some format conversions may be lossy'''. To change formats, select from the list provided in the File Format column. A dataset's filepath and filename may be edited to save the dataset in a location different from that specified. &lt;br /&gt;
&lt;br /&gt;
'''Supported formats:''' Formats that can be saved include:&lt;br /&gt;
* Volumes&lt;br /&gt;
** NRRD (.nrrd)&lt;br /&gt;
** NRRD (.nhdr)&lt;br /&gt;
** MetaImage (.mhd)&lt;br /&gt;
** MetaImage (.mha)&lt;br /&gt;
** VTK (.vtk)&lt;br /&gt;
** Analyze (.hdr)&lt;br /&gt;
** Analyze (.img)&lt;br /&gt;
** Analyze (.img.gz)&lt;br /&gt;
** BMP (.bmp, .BMP)&lt;br /&gt;
** BioRad (.pic)&lt;br /&gt;
** Brains2 (.mask)&lt;br /&gt;
** GIPL (.gipl, .gipl.gz)&lt;br /&gt;
** JPEG (.jpg, .jpeg, .JPG, .JPEG)&lt;br /&gt;
** LSM (.lms, .LSM)&lt;br /&gt;
** NifTI (.nia)&lt;br /&gt;
** NifTI (.nii, .nii.gz)&lt;br /&gt;
** PNG (.png, .PNG)&lt;br /&gt;
** Stimulate (.spr)&lt;br /&gt;
** TIFF (.tiff, .tif, .TIFF, .TIF)&lt;br /&gt;
* Models&lt;br /&gt;
** Poly Data (.vtk)&lt;br /&gt;
** XML Poly Data (.vtp)&lt;br /&gt;
** STL (.stl)&lt;br /&gt;
* Fiducials&lt;br /&gt;
** Fiducial List CSV (.fcsv)&lt;br /&gt;
** Text (.txt)&lt;br /&gt;
* Transforms&lt;br /&gt;
** Transform (.tfm)&lt;br /&gt;
** Text (.txt)&lt;br /&gt;
&lt;br /&gt;
'''Saving data:''' Finally, selecting the ''Save Selected'' button will launch the scene/data saving process, and ''Cancel'' will abort it.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Close Scene:''' &lt;br /&gt;
&lt;br /&gt;
This command closes the current scene and resets the application state.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Exit'''&lt;br /&gt;
&lt;br /&gt;
This command exits Slicer.&lt;br /&gt;
&lt;br /&gt;
== Edit menu ==&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Set Home'''&lt;br /&gt;
&lt;br /&gt;
This command sets a user's 'home module', which is the module displayed by default each time the Slicer application is started. The home module is saved in the Application Registry.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Undo''' &lt;br /&gt;
&lt;br /&gt;
This command undoes the history of undoable commands, from last to first. &lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Redo''' &lt;br /&gt;
&lt;br /&gt;
This command re-does the history of commands most recently undone, from last to first.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Edit Box''' &lt;br /&gt;
&lt;br /&gt;
This command raises the Edit-box, a lightweight image editing tool.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;New Fiducial List'''&lt;br /&gt;
 &lt;br /&gt;
This command creates a new list of fiducial points.&lt;br /&gt;
&lt;br /&gt;
==View menu ==&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Manage Extensions:'''&lt;br /&gt;
&lt;br /&gt;
This [[Modules::ExtensionsManagementWizard-Documentation-3.4 |Extensions Management Wizard]] provides status and information about available extensions for 3.4&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Cache &amp;amp; RemoteIO Manager:'''&lt;br /&gt;
&lt;br /&gt;
The Cache and Remote Data Handling interface provides status and information about all remote data transfers, and allows some control over the local cache. Remote I/O and Cache preferences can also be set in the Application Settings Interface, described next. Whether you set preferences here or there, they are saved in the Application Registry so that your settings are preserved each time you start up the Slicer Application.&lt;br /&gt;
&lt;br /&gt;
The pop-up interface is shown below. Checkbuttons at the top left provide choices about download and caching behavior, and the cache directory, cache size limit, and cache free space buffer can be set at the interface bottom. Icon buttons at the top right allow global operations on all data transfers (cache clearing and transfer cancellation) and display updates (transfer panel cleanup and cache report refreshing). Each data transfer is listed in the transfer panel along with some information about its type and status. &lt;br /&gt;
&lt;br /&gt;
[[image:RemoteIOGUIMap.png]]&lt;br /&gt;
&lt;br /&gt;
Below, all of the Cache &amp;amp; Remote Data I/O Manager icons are listed and described:&lt;br /&gt;
&lt;br /&gt;
[[image:RemoteIOIcons.png |center ]]&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Application Settings Interface:'''&lt;br /&gt;
&lt;br /&gt;
The Application Settings interface provides options for saving many of Slicer's Interface and Remote Data Handling options to the Application Registry, so they are preserved across sessions. The first time you start the application, it is recommended that you browse these settings and select options that you prefer. Some of the options provided in the interface are listed below:&lt;br /&gt;
&lt;br /&gt;
* ''Slicer Settings'' allow you to specify whether Slicer should confirm on delete, and set the location for other applications that Slicer may need to use (Firefox, Zip, ''etc.''). &lt;br /&gt;
* ''Font Settings'' options allows you to choose among several fonts and relative font sizes to be displayed in the GUI.&lt;br /&gt;
* ''Module Settings'' options allow you to select a Temporary directory, a home module (that will be displayed each time Slicer starts up) and whether Slicer should include loadable and command-line modules on startup.&lt;br /&gt;
* ''Remote Data Handling Settings'' options allow the specification of Cache and Remote Data I/O settings which are also configurable from the Cache and Remote Data I/O Manager described above.&lt;br /&gt;
&lt;br /&gt;
[[image:AppSettingsGUIMap.png]]&lt;br /&gt;
&lt;br /&gt;
==Window menu ==&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Hide/Show Main Panel (Hotkey = F5):'''&lt;br /&gt;
 &lt;br /&gt;
This command collapses or expands the GUI panel and allows Slicer's viewers to occupy the entire application window, as shown below in Application Layouts figure C.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Hide/Show Bottom Panel (Hotkey = F6):'''&lt;br /&gt;
 &lt;br /&gt;
This command collapses or expands the bottom split-panel in which Slice viewers are conventionally displayed, allowing the 3D view to occupy the vertical extent of the application window. The behavior of this command will vary, and may not be appropriate, depending on the selected layout (-- available layouts are described below.)&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Toolbars:'''&lt;br /&gt;
&lt;br /&gt;
This command allows hiding or exposing sub-toolbars in the application toolbars, including the Load/Save toolbar, the undo/redo toolbar, the layout configuration, and the mouse mode toolbar.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Log Window (Hotkey = Ctrl+Alt+E):'''&lt;br /&gt;
&lt;br /&gt;
This command raises the error log display.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Tcl Interactor (Hotkey = Ctrl+T):'''&lt;br /&gt;
 &lt;br /&gt;
This command raises the Tcl interactor for scripted interaction with Slicer data:&lt;br /&gt;
&lt;br /&gt;
[[image:TclInteractor.png |center ]]&lt;br /&gt;
&lt;br /&gt;
==Help menu ==&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;Browse Tutorials:'''&lt;br /&gt;
&lt;br /&gt;
Raises Slicer's training page in mozilla firefox web browser (Note: you will need to have specified the location of Mozilla Firefox executable in Slicer's Application Settings Interface: '''Application Settings-&amp;gt;Slicer Settings''').&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;About Slicer3:'''&lt;br /&gt;
&lt;br /&gt;
Provides a description of the Slicer3 effort and its support.&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;Keyboard Shortcuts:'''&lt;br /&gt;
&lt;br /&gt;
Raises a window that lists commonly-used keyboard shortcuts.&lt;br /&gt;
&lt;br /&gt;
==Feedback menu ==&lt;br /&gt;
'''Note: for all commands in the Feedback Menu, you will need to have specified the location of your Mozilla Firefox executable in Slicer's Application Settings Interface: Application Settings-&amp;gt;Slicer Settings) so Slicer knows how to launch the web browser.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Report a Bug:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that any bug you encounter can quickly and easily be reported. Be sure to select the appropriate category for the bug and estimate its severity. It's recommended that you provide as much information as you can so that the bug can be reproduced by the development team.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Report a Usability Issue:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that any usability issue you encounter can quickly be captured. Be sure to select the &amp;quot;usability&amp;quot; category for the issue and estimate its severity. We request that you describe the way in which the usability issue is impacting your work so that the usability and development team can address the issue appropriately. Suggestions and ideas are welcome!&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Make a Feature Request:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that community feature requests can easily be collected. We request that you clearly mark your submission as a &amp;quot;feature request&amp;quot; in the description field of the form.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Community:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.slicer.org/slicerWiki/index.php/Slicer3:VisualBlog where you can post screenshots of interesting ways you are using the Slicer3 software package in your research and share them with the Slicer community.&lt;br /&gt;
&lt;br /&gt;
= Application Toolbar =&lt;br /&gt;
&lt;br /&gt;
Slicer's toolbar provides quick access to centralized load / save functionality, options for searching for and navigating among modules, undo/redo capability, ability to select different application layouts and change among mouse modes. Using and indicating mouse modes in Slicer is still under development, so this part of the toolbar will likely change in future releases. For now, &amp;quot;Mouse place&amp;quot; is used to create new objects, like fiducial points. &amp;quot;Mouse pick&amp;quot; is intended for selecting objects. &amp;quot;Transform view&amp;quot; is the default mode, used to pan, zoom and rotate the camera in the 3D viewer. Individual icons in the toolbar are labeled below.&lt;br /&gt;
&lt;br /&gt;
[[image:AppToolbarMap.png]]&lt;br /&gt;
&lt;br /&gt;
The Window-&amp;gt;Toolbars submenu allows showing/hiding parts of this toolbar, including the Load/Save toolbar, the undo/redo toolbar, the layout configuration, and the mouse mode toolbar.&lt;br /&gt;
&lt;br /&gt;
= Module GUI Panel =&lt;br /&gt;
&lt;br /&gt;
=='''Conventions and window position:'''==&lt;br /&gt;
By default, the Module GUI panel is located on the left of the application window. The panel that contains the Module GUI, Slices Control GUI and 3D Viewer Control GUI (both described below) can be moved to the right side also by selecting that option from the layout menu on the toolbar, if that working configuration is found to be more convenient. Each Slicer module populates the Module GUI panel with its interface; all modules have a Help &amp;amp; Acknowledgement frame that presents brief help text and pointers to additional information, and appropriate acknowledgement for the work as shown in the figure below. &lt;br /&gt;
&lt;br /&gt;
=='''Collapsing and expanding frames:'''==&lt;br /&gt;
Each module GUI contains its functionality inside collapsing and expanding frames, also shown below, to minimize the need to scroll among individual blocks of functionality within a module. The frames can be collapsed or expanded by clicking in the title frame. The Slices Control and 3D Viewer Control GUI panels also can be collapsed to make more space for a module GUI. &lt;br /&gt;
&lt;br /&gt;
Brief '''Help Text''' and '''Module Attribution and Acknowledgements''' can be found in the topmost panel in any module.&lt;br /&gt;
&lt;br /&gt;
[[image:ModuleGUIPanel.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= Slice Viewer Control Panel =&lt;br /&gt;
The Slice Viewer Control Panel allows configuration of all Slice GUIs at once. The functionality represented by icons in Slicer Version 3.2 is described below:&lt;br /&gt;
&lt;br /&gt;
[[image:SCGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= 3D Viewer Control Panel =&lt;br /&gt;
&lt;br /&gt;
The 3D Viewer Control Panel provides many options for configuring the 3D viewer. The left-most panel allows the view to be oriented along any of the six principle axes ('''S'''uperior, '''I'''nferor, '''A'''nterior, '''P'''osterior, '''L'''eft or '''R'''ight). Axis symbols highlight on mouse-over. The functionality included in the panel represented by icons and checkboxes is described in the diagram below. Finally, the rightmost viewer duals as a birds-eye-view display of the entire scene, or a slice magnifier window when the mouse moves over any of the slice windows.&lt;br /&gt;
&lt;br /&gt;
[[image:VCGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
== Stereoscopic and Kinetic Depth ==&lt;br /&gt;
The 3D Viewer provides a number of options for assessing depth and layout in complicated scenes. The stereo viewing pull-down menu, labeled &amp;quot;M&amp;quot; in the schmatic above, provides several stereo viewing options, and the view rock (labeled &amp;quot;O&amp;quot;) and view spin (labeled &amp;quot;N&amp;quot;) animate the scene to help clarify feature shape, depth and layout.&lt;br /&gt;
&lt;br /&gt;
== Screen Captures (&amp;quot;Screenshots&amp;quot;)==&lt;br /&gt;
Screen captures of the 3D Viewer can be saved by selecting the icon labeled &amp;quot;D&amp;quot; in the schematic above. This raises the Screen Capture interface (shown below) that allows you to specify a save destination, a filename, version number, image format and exposes the option for overwriting existing files.&lt;br /&gt;
&lt;br /&gt;
[[image:VCGUI-Screenshots.png |center ]]&lt;br /&gt;
&lt;br /&gt;
== Scene Snapshots==&lt;br /&gt;
Scene snapshots provide a way to record particular compositions of a scene. These compositions are saved with the scene and can be restored for later inspection. Among the things recorded in each snapshot are: &lt;br /&gt;
* Model visibility,&lt;br /&gt;
* Volume display threshold, window and level settings, &lt;br /&gt;
* Slice visibility in the 3D view.&lt;br /&gt;
&lt;br /&gt;
To create or restore a scene snapshot:&lt;br /&gt;
* Click on the camera icon (labeled &amp;quot;H&amp;quot; in the schematic above) to record a scenesnapshot. &lt;br /&gt;
* Use the pull down menu (labeled &amp;quot;L&amp;quot; in the schematic above) to select from a list of existing snapshots. &lt;br /&gt;
* Click on the arrow icon to restore the snapshot.&lt;br /&gt;
* You can also click on the trashcan icon to delete the snapshot.&lt;br /&gt;
&lt;br /&gt;
[[image:SceneSnapshots.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= Slicer Viewers = &lt;br /&gt;
In this section, Slicer's Slice Viewers and Main 3D Viewer are described, and options for configuring their layout and display of information.&lt;br /&gt;
&lt;br /&gt;
== Slice Viewers (and their Controllers) ==&lt;br /&gt;
&lt;br /&gt;
Slicer's three main Slice Viewers are color-coded Red, Yellow and Green. By default, these correspond to '''Axial''', '''Saggital''' and '''Coronal''' slice orientations respectively, but this can be modified by a user. In Slicer's '''Compare View''' layout (described a little later), the Slice Viewers are color-coded Orange.&lt;br /&gt;
&lt;br /&gt;
All Slice viewers have their own Slice Controller, which can be expanded or collapsed by clicking in the colored bar at their top, for convenience. The Red Viewer is shown below, expanded and collapsed as described. Note that corner annotations are displayed when the mouse hovers over any viewer.&lt;br /&gt;
&lt;br /&gt;
[[image:SliceControllerGUICollapseAndExpand.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Slice orientation and Oblique reformats===&lt;br /&gt;
On each Slice Viewer, an '''Orientation''' menu button in the upper left of the control panel provides the option to display an  &amp;quot;Axial&amp;quot;, &amp;quot;Coronal&amp;quot;, &amp;quot;Sagittal&amp;quot;, or &amp;quot;Reformat&amp;quot; slice orientation in the Viewer.  &lt;br /&gt;
&lt;br /&gt;
[[image:SliceGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
Slice viewers can be used to specify oblique reformats in two ways:&lt;br /&gt;
* first by using the &amp;quot;Reformat&amp;quot; orientation and CTRL-Right-Button-Move (subject to change and something of an &amp;quot;art&amp;quot; to control).&lt;br /&gt;
* and second by selecting the '''Show Reformat Widget''' option ([[image:SliceControllerShowReformatWidget.png]]) from the Slice Controller's '''More Options''' menu ([[image:SliceControllerMoreOptions.png]]), and interacting with the widget. The widget can be toggled off using the menu's '''Hide Reformat Widget''' option ([[image:SliceControllerHideReformatWidget.png]]). Using this widget's interactive box &amp;amp; arrow to reformat the slice plane (illustrated below) causes the Orientation selector to display the &amp;quot;Reformat&amp;quot; orientation, and the Slice Viewer to display the reformatted plane.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ReformatWidget.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Linking Control of Slice Viewers===&lt;br /&gt;
&lt;br /&gt;
Control of slice viewers can be linked to save time setting them up and manipulating their display individually. The icons shown below, found in the leftmost of each Slice Controller's toolbar, toggle linking and unlinking of the viewers.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-SliceLink.png]]&lt;br /&gt;
&lt;br /&gt;
When Slice Viewers are linked, the &amp;quot;linked&amp;quot; icon ([[image:AppDoc-SlicesLinked.png]])is displayed. Clicking the icon-button will unlink the Viewers, and will display the &amp;quot;Unlinked&amp;quot; icon ([[image:AppDoc-SlicesUnlinked.png]]). When the Slice Viewers are linked, many but not all of the controllers' options apply to all viewers. The following controls are linked:&lt;br /&gt;
&lt;br /&gt;
* Orientation&lt;br /&gt;
* FG, BG, Label selectors&lt;br /&gt;
* Visibility&lt;br /&gt;
* Fit To Window&lt;br /&gt;
* Adjust Label Map Opacity&lt;br /&gt;
* Show/Hide Label Volume Outlines&lt;br /&gt;
* Show/Hide Reformat Widget&lt;br /&gt;
&lt;br /&gt;
===Slice Plane Visibility in 3D Viewer===&lt;br /&gt;
&lt;br /&gt;
The Slices shown in each of the Slice Viewers may be displayed in the Main 3D Viewer as well. Their visibility in the 3D Viewer is controlled with the '''Visibility''' icon button in the Slice Controllers, as shown in the figure below. When Slices are visible in the 3D Viewer, the &amp;quot;visible&amp;quot; icon ([[image:AppDoc-SlicesVisible.png]])is displayed. Clicking the icon-button will hide the Slices in the 3D Viewer, and will display the &amp;quot;Invisible&amp;quot; icon ([[image:AppDoc-SlicesInvisible.png]]). &lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-SliceVisibility.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Other Slice GUI options===&lt;br /&gt;
&lt;br /&gt;
The Slice controllers offer other options as well, available under the '''More Options''' menubutton ([[image:SliceControllerMoreOptions.png]]). Options here include some of those available in the '''Slices Controller GUI''' and some additional. These options, each shown in the figures '''A - H''' below, include:&lt;br /&gt;
&lt;br /&gt;
* A. Fit a slice to the size of a Viewer's window&lt;br /&gt;
* B. Adjust the opacity of a label map&lt;br /&gt;
* C. Show/Hide outlines around labels in a label map&lt;br /&gt;
* D. Show/Hide the Slice Reformat Widget&lt;br /&gt;
* E. Select options for compositing slice layers&lt;br /&gt;
* F. Choose manual or automatic slice spacing modes&lt;br /&gt;
* G. Create a lightbox view within a Slice Viewer&lt;br /&gt;
* H. Adjust the display of Foreground, Background or Label layers.&lt;br /&gt;
&lt;br /&gt;
[[image:SliceGUIMoreMap.png]]&lt;br /&gt;
&lt;br /&gt;
===Configuring Slice Viewers when the Controllers are collapsed ===&lt;br /&gt;
&lt;br /&gt;
In Slicer's '''Slices Module''', all Slice Viewers' Slice Controllers are arrayed in a vertical stack; When screen real estate must be maximized, the individual Slice Viewers' Controllers can be collapsed and the GUI panel's controllers can be used to manipulate the Viewers instead. The Slices Module's GUI panel is shown below.&lt;br /&gt;
&lt;br /&gt;
[[image:SlicesGUIPanel.png |center ]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Main 3D Viewer ==&lt;br /&gt;
&lt;br /&gt;
=== Default elements and their visibility===&lt;br /&gt;
&lt;br /&gt;
Slicer's Main 3D Viewer displays a three-dimensional view of the scene. By default, the scene includes some elements for spatial reference including a 3D wireframe cube centered around the origin (0,0,0) and labels along each of the principle axes ('''R'''ight, '''L'''eft, '''S'''uperior, '''I'''nferior, '''A'''nterior, and '''P'''osterior). Slicer's default blue background color, as well as the visibility of the spatial references in the view, can be modified in the View Control GUI panel's visibility menu, as shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-VCGuiVisibility.png]]&lt;br /&gt;
&lt;br /&gt;
=== Interacting ===&lt;br /&gt;
&lt;br /&gt;
You can adjust the view in the Main 3D Viewer using the mouse or keyboard (for information on the latter, please see the Keyboard Shortcuts section):&lt;br /&gt;
&lt;br /&gt;
* '''Zoom in:''' Right-mouse-button click-and-drag toward you. (Imagine pulling the scene closer)&lt;br /&gt;
* '''Zoom out:''' Right-mouse-button click-and-drag away from you. (Imagine pushing the scene away)&lt;br /&gt;
* '''Pan''' (shift the look-at point): Middle-mouse-button click-and-drag left, right, up or down.&lt;br /&gt;
* '''Rotate Around''' a look-at point: Left-mouse-button click-and-drag.&lt;br /&gt;
&lt;br /&gt;
If you need more precise control, or if the view gets into some hard-to-manage configuration, the View Control GUI panel can be used to reset the look-from and look-at point in a manageable way:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-VCGuiSetView.png]]&lt;br /&gt;
&lt;br /&gt;
=== Window and layout configurations ===&lt;br /&gt;
&lt;br /&gt;
Slicer can be configured to show or hide the Module GUI panel, and to display it on the left or right side of the Viewers. These options are accessed as follows:&lt;br /&gt;
&lt;br /&gt;
* Show/Hide Module GUI Panel: F5-key or Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]])-&amp;gt;Toggle GUI panel visibility&lt;br /&gt;
* Move Module GUI Panel to the Left/Right: Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]])-&amp;gt;Toggle GUI panel L/R&lt;br /&gt;
* Show/Hide Bottom Panel: F6-key (this option is only really useful in Slicer's Conventional View)&lt;br /&gt;
&lt;br /&gt;
[[image:AppGUIBasicConfigure.png]]&lt;br /&gt;
&lt;br /&gt;
In addition, there are a number of ways to arrange the Slice and 3D Viewers. We hope to offer a more extensible suite of configuration options in the future. At present, these options are available from Slicer's Application Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]]), and are illustrated below:&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
&lt;br /&gt;
[[image:AppLayouts.png]]&lt;br /&gt;
&lt;br /&gt;
= Error Log =&lt;br /&gt;
&lt;br /&gt;
Finally, the application has an accessible error log in the event of unexpected behavior or error messages -- this readout is useful for reporting bugs or usability problems back to the Slicer Development Team. The error log can be raised in the following ways:&lt;br /&gt;
&lt;br /&gt;
* Typing '''Ctrl+Alt+E'''&lt;br /&gt;
* Menubar's '''Window-&amp;gt;Error Log'''&lt;br /&gt;
* Clicking the '''Error Log icon''', which is displayed only if any error reports are present, and as shown below.&lt;br /&gt;
&lt;br /&gt;
[[image:RaiseErrorLog.png]]&lt;br /&gt;
&lt;br /&gt;
[[image:ErrorLog.png]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
= Status Text and Progress Bar =&lt;br /&gt;
&lt;br /&gt;
For some operations, loading, saving or processing may take awhile; Slicer may post status text at the bottom of the Application's window (shown below) that helps you to understand what it's working on. This readout isn't available as often as it should be; we hope to address this usability issue in future software releases. If you encounter any situation in which a status update would be especially useful but none exists, please report your discovery to Slicer's bug tracker as a usability issue.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-StatusText.png  ]]&lt;br /&gt;
&lt;br /&gt;
Progress is also displayed during processing operations. One progress readout commonly used by command-line modules is found in the lower right corner of the Slicer Window in the Progress Gauge, shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ProgressBar.png |center ]]&lt;br /&gt;
&lt;br /&gt;
Some Slicer modules also use a pop-up progress dialog, which assumes &amp;quot;focus&amp;quot; and prevents you from interacting with Slicer until the processing is finished; the dialog appears as below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ProgressDialog.png |center ]]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Modules:MainApplicationGUI-Documentation-3.4&amp;diff=9492</id>
		<title>Modules:MainApplicationGUI-Documentation-3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Modules:MainApplicationGUI-Documentation-3.4&amp;diff=9492"/>
		<updated>2009-05-08T21:14:59Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* View menu */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[Documentation-3.4#Main_GUI|Return to Slicer Documentation]]&lt;br /&gt;
&lt;br /&gt;
'''Overview'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Slicer3's main desktop interface provides top-level access to most commonly-used features, and organizes them into logical groupings. These groups of features are presented in a number of interface panels on the GUI, as is illustrated in the basic layout below. The interface is designed to be easy to learn and remember, to ease navigation of Slicer's large (and growing) functionality, and to easily collapse and hide when you don't need to see it. Figures A through I in the &amp;quot;Individual frames&amp;quot; gallery a little further down on this page provide richer detail and will be described in the following sections.&lt;br /&gt;
&lt;br /&gt;
[[image:SlicerGUIIntro.png ]]&lt;br /&gt;
&lt;br /&gt;
As shown above, the logical groupings of Slicer's interface elements include:&lt;br /&gt;
* The Application Menubar&lt;br /&gt;
* The Application Toolbar&lt;br /&gt;
* The Main GUI Panel, which consists of:&lt;br /&gt;
** Slicer's Logo Panel&lt;br /&gt;
** The Module GUI Panel&lt;br /&gt;
** The Slice Viewer Controls&lt;br /&gt;
** The 3D Viewer Controls&lt;br /&gt;
* The 3D Viewer&lt;br /&gt;
* Three Main Slice Viewers (Red, Yellow, and Green)and additional Slice Viewers&lt;br /&gt;
* The Message Bar and Progress Gauge&lt;br /&gt;
* And the Error Log Button&lt;br /&gt;
&lt;br /&gt;
An overview of the functionality provided in each of these interface elements is provided below.&lt;br /&gt;
&lt;br /&gt;
=Individual Panels=&lt;br /&gt;
&lt;br /&gt;
&amp;lt;gallery perrow=&amp;quot;3&amp;quot; widths=&amp;quot;300px&amp;quot; heights=&amp;quot;200px&amp;quot;&amp;gt;&lt;br /&gt;
Image:AppGUIMap.png | '''Figure A.''' Schematic of the [[ Modules:MainApplicationGUI-Documentation-3.2#Main_Application_GUI_organization | main application GUI ]]&lt;br /&gt;
Image:AppToolbarMap.png | '''Figure B.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#Application_Toolbar | Application Toolbar ]]&lt;br /&gt;
Image:SCGUIMap.png | '''Figure C.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewer_Control_Panel | Controller for all Slice Viewers ]]&lt;br /&gt;
Image:VCGUIMap.png | '''Figure D.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#3D_Viewer_Control_Panel | Controller for the 3D Viewer ]]&lt;br /&gt;
image:SliceGUIMap.png | '''Figure E.''' Schematic of a [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewers_.26_Controllers | Slice Viewer and Slice Controller]]&lt;br /&gt;
Image:ModuleGUIPanel.png | '''Figure F.''' Schematic of an [[Modules:MainApplicationGUI-Documentation-3.4#Module_GUI_Panel | expanding/collapsing module GUI panel ]]&lt;br /&gt;
Image:SliceGUIMoreMap.png | '''Figure G.''' Schematic of [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewers_.26_Controllers | Slice Viewer additional options ]]&lt;br /&gt;
Image:AppSettingsGUIMap.png | '''Figure H.''' Schematics of the [[Modules:MainApplicationGUI-Documentation-3.2#View-.3EApplication_Settings_Interface: | Application Settings Interface ]]&lt;br /&gt;
Image:RemoteIOGUIMap.png | '''Figure I.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#View-.3ECache_.26_RemoteIO_Manager: | Remote Data Handling Interface ]]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Application Menubar =&lt;br /&gt;
The Application menubar is at the very top of Slicer3's main window, as noted above and in Figure A. Its menus and functionality are briefly listed below.&lt;br /&gt;
&lt;br /&gt;
== File menu ==&lt;br /&gt;
&lt;br /&gt;
Several loading options are available from the file menu. Below is a '''general overview''' of these options. For more details and suggestions for common use cases, see [[ Modules:Loading-Data-3.4 | Data loading details for Slicer3.4]]. For information about accessing the functionality described below and loading other types of data (like transforms, fiducial lists, color tables, DTI fiber bundles ''etc''.) through the Data Module, see [[Modules:DataModule-3.4 | Slicer's Data Module documentation]].&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Load Scene:''' &lt;br /&gt;
&lt;br /&gt;
This command raises a file browser (shown below). Slicer's file browser has a 'favorites' icon that allows you to save often-visited directories on the browser's left panel. Other features, including icons that allow you to navigate your browsing history, pop up a level in the directory structure (or folder hierarchy) and create new folders. To load a scene, navigate to a file of the appropriate format (.mrml, .xcat (XCEDE catalog file), or .xml (Slicer2 scene file) and select it for loading into Slicer. '''The command first clears any existing scene''' in Slicer and '''resets the application state'''.&lt;br /&gt;
&lt;br /&gt;
[[image:FileBrowser.png]]&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Import Scene:'''&lt;br /&gt;
&lt;br /&gt;
This command raises the same file browser shown above. Navigate to and select a scene file to be added to the existing Slicer scene. '''(The existing scene is not cleared)'''.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Add Data:'''&lt;br /&gt;
&lt;br /&gt;
This command raises an &amp;quot;Add Data&amp;quot; widget (shown below) that allows you to select individual datasets to add to the existing scene. This load option is most useful when you want to load many different data types at once (volumes, models, ''etc.'') which may not yet be described by a scene file. It exposes the following functionality:&lt;br /&gt;
&lt;br /&gt;
* The &amp;quot;Add Directory&amp;quot; button adds all files within the selected directory to the file list.&lt;br /&gt;
* The &amp;quot;Add File(s)&amp;quot; button adds all selected files to the file list.&lt;br /&gt;
* The array of buttons across the top allow you to select and deselect files in the file list, remove selected files from the list, or describe how files should be loaded.&lt;br /&gt;
* The &amp;quot;Apply&amp;quot; button loads all datasets in the list, and&lt;br /&gt;
* The &amp;quot;Cancel&amp;quot; button aborts the entire load.&lt;br /&gt;
&lt;br /&gt;
[[image:AppAddData.png]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Add Volume:''' &lt;br /&gt;
&lt;br /&gt;
This command raises an &amp;quot;Add Volume&amp;quot; widget (shown below) that allows you to select a volumetric dataset to add to the existing scene. The &amp;quot;Volume Options&amp;quot; panel can be used to clarify how a selected dataset should be loaded and displayed. This load option is particularly useful for loading DICOM data, for which its DICOM information parsing panel can be helpful.&lt;br /&gt;
&lt;br /&gt;
[[image:AppAddVolume.png]]&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Save:'''&lt;br /&gt;
&lt;br /&gt;
This command displays the &amp;quot;Save Data&amp;quot; widget, which offers many options for saving a scene and/or individual datasets. The widget is shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppSaveData.png]]&lt;br /&gt;
&lt;br /&gt;
'''Specifying a scene file to save:''' The ''Scene Description'' entry is always listed in the top row of the table. If a scene has already been loaded from a MRML file, then its filename is presented as the default choice. To save the scene into a '''new''' MRML file, either provide an alternate file name, or provide a new Data Directory.  &lt;br /&gt;
&lt;br /&gt;
'''Indicating new and unsaved datasets:''' When the panel is first displayed, all datasets which have been newly created or modified since the scene was saved are checked by default in the ''Save'' column. Any datasets in the scene can be checked/unchecked for saving/not saving using the checkboxes provided in this column. The icon buttons in the top left corner (from left to right) of the window provide shortcuts to modify the default selection:&lt;br /&gt;
&lt;br /&gt;
* '''Select Scene and Modified Data''', &lt;br /&gt;
* '''Select Modified Data'''only,&lt;br /&gt;
* '''Select All''', and&lt;br /&gt;
* '''Select None'''.&lt;br /&gt;
&lt;br /&gt;
These icons are shown and annotated below, under the SaveData illustration. Any individual checkbox can also be used to modify the selection state.  &lt;br /&gt;
&lt;br /&gt;
[[image:AppSaveDataIcons.png]]&lt;br /&gt;
&lt;br /&gt;
'''Converting to other data formats:''' Any dataset can be converted to a different (supported) format by editing the filename extension. '''Note that some format conversions may be lossy'''. To change formats, select from the list provided in the File Format column. A dataset's filepath and filename may be edited to save the dataset in a location different from that specified. &lt;br /&gt;
&lt;br /&gt;
'''Supported formats:''' Formats that can be saved include:&lt;br /&gt;
* Volumes&lt;br /&gt;
** NRRD (.nrrd)&lt;br /&gt;
** NRRD (.nhdr)&lt;br /&gt;
** MetaImage (.mhd)&lt;br /&gt;
** MetaImage (.mha)&lt;br /&gt;
** VTK (.vtk)&lt;br /&gt;
** Analyze (.hdr)&lt;br /&gt;
** Analyze (.img)&lt;br /&gt;
** Analyze (.img.gz)&lt;br /&gt;
** BMP (.bmp, .BMP)&lt;br /&gt;
** BioRad (.pic)&lt;br /&gt;
** Brains2 (.mask)&lt;br /&gt;
** GIPL (.gipl, .gipl.gz)&lt;br /&gt;
** JPEG (.jpg, .jpeg, .JPG, .JPEG)&lt;br /&gt;
** LSM (.lms, .LSM)&lt;br /&gt;
** NifTI (.nia)&lt;br /&gt;
** NifTI (.nii, .nii.gz)&lt;br /&gt;
** PNG (.png, .PNG)&lt;br /&gt;
** Stimulate (.spr)&lt;br /&gt;
** TIFF (.tiff, .tif, .TIFF, .TIF)&lt;br /&gt;
* Models&lt;br /&gt;
** Poly Data (.vtk)&lt;br /&gt;
** XML Poly Data (.vtp)&lt;br /&gt;
** STL (.stl)&lt;br /&gt;
* Fiducials&lt;br /&gt;
** Fiducial List CSV (.fcsv)&lt;br /&gt;
** Text (.txt)&lt;br /&gt;
* Transforms&lt;br /&gt;
** Transform (.tfm)&lt;br /&gt;
** Text (.txt)&lt;br /&gt;
&lt;br /&gt;
'''Saving data:''' Finally, selecting the ''Save Selected'' button will launch the scene/data saving process, and ''Cancel'' will abort it.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Close Scene:''' &lt;br /&gt;
&lt;br /&gt;
This command closes the current scene and resets the application state.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Exit'''&lt;br /&gt;
&lt;br /&gt;
This command exits Slicer.&lt;br /&gt;
&lt;br /&gt;
== Edit menu ==&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Set Home'''&lt;br /&gt;
&lt;br /&gt;
This command sets a user's 'home module', which is the module displayed by default each time the Slicer application is started. The home module is saved in the Application Registry.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Undo''' &lt;br /&gt;
&lt;br /&gt;
This command undoes the history of undoable commands, from last to first. &lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Redo''' &lt;br /&gt;
&lt;br /&gt;
This command re-does the history of commands most recently undone, from last to first.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Edit Box''' &lt;br /&gt;
&lt;br /&gt;
This command raises the Edit-box, a lightweight image editing tool.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;New Fiducial List'''&lt;br /&gt;
 &lt;br /&gt;
This command creates a new list of fiducial points.&lt;br /&gt;
&lt;br /&gt;
==View menu ==&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Manage Extensions:'''&lt;br /&gt;
&lt;br /&gt;
This [[Modules::ExtensionsManagementWizard-Documentation-3.4]] provides status and information about available extensions for 3.4&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Cache &amp;amp; RemoteIO Manager:'''&lt;br /&gt;
&lt;br /&gt;
The Cache and Remote Data Handling interface provides status and information about all remote data transfers, and allows some control over the local cache. Remote I/O and Cache preferences can also be set in the Application Settings Interface, described next. Whether you set preferences here or there, they are saved in the Application Registry so that your settings are preserved each time you start up the Slicer Application.&lt;br /&gt;
&lt;br /&gt;
The pop-up interface is shown below. Checkbuttons at the top left provide choices about download and caching behavior, and the cache directory, cache size limit, and cache free space buffer can be set at the interface bottom. Icon buttons at the top right allow global operations on all data transfers (cache clearing and transfer cancellation) and display updates (transfer panel cleanup and cache report refreshing). Each data transfer is listed in the transfer panel along with some information about its type and status. &lt;br /&gt;
&lt;br /&gt;
[[image:RemoteIOGUIMap.png]]&lt;br /&gt;
&lt;br /&gt;
Below, all of the Cache &amp;amp; Remote Data I/O Manager icons are listed and described:&lt;br /&gt;
&lt;br /&gt;
[[image:RemoteIOIcons.png |center ]]&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Application Settings Interface:'''&lt;br /&gt;
&lt;br /&gt;
The Application Settings interface provides options for saving many of Slicer's Interface and Remote Data Handling options to the Application Registry, so they are preserved across sessions. The first time you start the application, it is recommended that you browse these settings and select options that you prefer. Some of the options provided in the interface are listed below:&lt;br /&gt;
&lt;br /&gt;
* ''Slicer Settings'' allow you to specify whether Slicer should confirm on delete, and set the location for other applications that Slicer may need to use (Firefox, Zip, ''etc.''). &lt;br /&gt;
* ''Font Settings'' options allows you to choose among several fonts and relative font sizes to be displayed in the GUI.&lt;br /&gt;
* ''Module Settings'' options allow you to select a Temporary directory, a home module (that will be displayed each time Slicer starts up) and whether Slicer should include loadable and command-line modules on startup.&lt;br /&gt;
* ''Remote Data Handling Settings'' options allow the specification of Cache and Remote Data I/O settings which are also configurable from the Cache and Remote Data I/O Manager described above.&lt;br /&gt;
&lt;br /&gt;
[[image:AppSettingsGUIMap.png]]&lt;br /&gt;
&lt;br /&gt;
==Window menu ==&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Hide/Show Main Panel (Hotkey = F5):'''&lt;br /&gt;
 &lt;br /&gt;
This command collapses or expands the GUI panel and allows Slicer's viewers to occupy the entire application window, as shown below in Application Layouts figure C.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Hide/Show Bottom Panel (Hotkey = F6):'''&lt;br /&gt;
 &lt;br /&gt;
This command collapses or expands the bottom split-panel in which Slice viewers are conventionally displayed, allowing the 3D view to occupy the vertical extent of the application window. The behavior of this command will vary, and may not be appropriate, depending on the selected layout (-- available layouts are described below.)&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Toolbars:'''&lt;br /&gt;
&lt;br /&gt;
This command allows hiding or exposing sub-toolbars in the application toolbars, including the Load/Save toolbar, the undo/redo toolbar, the layout configuration, and the mouse mode toolbar.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Log Window (Hotkey = Ctrl+Alt+E):'''&lt;br /&gt;
&lt;br /&gt;
This command raises the error log display.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Tcl Interactor (Hotkey = Ctrl+T):'''&lt;br /&gt;
 &lt;br /&gt;
This command raises the Tcl interactor for scripted interaction with Slicer data:&lt;br /&gt;
&lt;br /&gt;
[[image:TclInteractor.png |center ]]&lt;br /&gt;
&lt;br /&gt;
==Help menu ==&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;Browse Tutorials:'''&lt;br /&gt;
&lt;br /&gt;
Raises Slicer's training page in mozilla firefox web browser (Note: you will need to have specified the location of Mozilla Firefox executable in Slicer's Application Settings Interface: '''Application Settings-&amp;gt;Slicer Settings''').&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;About Slicer3:'''&lt;br /&gt;
&lt;br /&gt;
Provides a description of the Slicer3 effort and its support.&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;Keyboard Shortcuts:'''&lt;br /&gt;
&lt;br /&gt;
Raises a window that lists commonly-used keyboard shortcuts.&lt;br /&gt;
&lt;br /&gt;
==Feedback menu ==&lt;br /&gt;
'''Note: for all commands in the Feedback Menu, you will need to have specified the location of your Mozilla Firefox executable in Slicer's Application Settings Interface: Application Settings-&amp;gt;Slicer Settings) so Slicer knows how to launch the web browser.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Report a Bug:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that any bug you encounter can quickly and easily be reported. Be sure to select the appropriate category for the bug and estimate its severity. It's recommended that you provide as much information as you can so that the bug can be reproduced by the development team.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Report a Usability Issue:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that any usability issue you encounter can quickly be captured. Be sure to select the &amp;quot;usability&amp;quot; category for the issue and estimate its severity. We request that you describe the way in which the usability issue is impacting your work so that the usability and development team can address the issue appropriately. Suggestions and ideas are welcome!&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Make a Feature Request:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that community feature requests can easily be collected. We request that you clearly mark your submission as a &amp;quot;feature request&amp;quot; in the description field of the form.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Community:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.slicer.org/slicerWiki/index.php/Slicer3:VisualBlog where you can post screenshots of interesting ways you are using the Slicer3 software package in your research and share them with the Slicer community.&lt;br /&gt;
&lt;br /&gt;
= Application Toolbar =&lt;br /&gt;
&lt;br /&gt;
Slicer's toolbar provides quick access to centralized load / save functionality, options for searching for and navigating among modules, undo/redo capability, ability to select different application layouts and change among mouse modes. Using and indicating mouse modes in Slicer is still under development, so this part of the toolbar will likely change in future releases. For now, &amp;quot;Mouse place&amp;quot; is used to create new objects, like fiducial points. &amp;quot;Mouse pick&amp;quot; is intended for selecting objects. &amp;quot;Transform view&amp;quot; is the default mode, used to pan, zoom and rotate the camera in the 3D viewer. Individual icons in the toolbar are labeled below.&lt;br /&gt;
&lt;br /&gt;
[[image:AppToolbarMap.png]]&lt;br /&gt;
&lt;br /&gt;
The Window-&amp;gt;Toolbars submenu allows showing/hiding parts of this toolbar, including the Load/Save toolbar, the undo/redo toolbar, the layout configuration, and the mouse mode toolbar.&lt;br /&gt;
&lt;br /&gt;
= Module GUI Panel =&lt;br /&gt;
&lt;br /&gt;
=='''Conventions and window position:'''==&lt;br /&gt;
By default, the Module GUI panel is located on the left of the application window. The panel that contains the Module GUI, Slices Control GUI and 3D Viewer Control GUI (both described below) can be moved to the right side also by selecting that option from the layout menu on the toolbar, if that working configuration is found to be more convenient. Each Slicer module populates the Module GUI panel with its interface; all modules have a Help &amp;amp; Acknowledgement frame that presents brief help text and pointers to additional information, and appropriate acknowledgement for the work as shown in the figure below. &lt;br /&gt;
&lt;br /&gt;
=='''Collapsing and expanding frames:'''==&lt;br /&gt;
Each module GUI contains its functionality inside collapsing and expanding frames, also shown below, to minimize the need to scroll among individual blocks of functionality within a module. The frames can be collapsed or expanded by clicking in the title frame. The Slices Control and 3D Viewer Control GUI panels also can be collapsed to make more space for a module GUI. &lt;br /&gt;
&lt;br /&gt;
Brief '''Help Text''' and '''Module Attribution and Acknowledgements''' can be found in the topmost panel in any module.&lt;br /&gt;
&lt;br /&gt;
[[image:ModuleGUIPanel.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= Slice Viewer Control Panel =&lt;br /&gt;
The Slice Viewer Control Panel allows configuration of all Slice GUIs at once. The functionality represented by icons in Slicer Version 3.2 is described below:&lt;br /&gt;
&lt;br /&gt;
[[image:SCGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= 3D Viewer Control Panel =&lt;br /&gt;
&lt;br /&gt;
The 3D Viewer Control Panel provides many options for configuring the 3D viewer. The left-most panel allows the view to be oriented along any of the six principle axes ('''S'''uperior, '''I'''nferor, '''A'''nterior, '''P'''osterior, '''L'''eft or '''R'''ight). Axis symbols highlight on mouse-over. The functionality included in the panel represented by icons and checkboxes is described in the diagram below. Finally, the rightmost viewer duals as a birds-eye-view display of the entire scene, or a slice magnifier window when the mouse moves over any of the slice windows.&lt;br /&gt;
&lt;br /&gt;
[[image:VCGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
== Stereoscopic and Kinetic Depth ==&lt;br /&gt;
The 3D Viewer provides a number of options for assessing depth and layout in complicated scenes. The stereo viewing pull-down menu, labeled &amp;quot;M&amp;quot; in the schmatic above, provides several stereo viewing options, and the view rock (labeled &amp;quot;O&amp;quot;) and view spin (labeled &amp;quot;N&amp;quot;) animate the scene to help clarify feature shape, depth and layout.&lt;br /&gt;
&lt;br /&gt;
== Screen Captures (&amp;quot;Screenshots&amp;quot;)==&lt;br /&gt;
Screen captures of the 3D Viewer can be saved by selecting the icon labeled &amp;quot;D&amp;quot; in the schematic above. This raises the Screen Capture interface (shown below) that allows you to specify a save destination, a filename, version number, image format and exposes the option for overwriting existing files.&lt;br /&gt;
&lt;br /&gt;
[[image:VCGUI-Screenshots.png |center ]]&lt;br /&gt;
&lt;br /&gt;
== Scene Snapshots==&lt;br /&gt;
Scene snapshots provide a way to record particular compositions of a scene. These compositions are saved with the scene and can be restored for later inspection. Among the things recorded in each snapshot are: &lt;br /&gt;
* Model visibility,&lt;br /&gt;
* Volume display threshold, window and level settings, &lt;br /&gt;
* Slice visibility in the 3D view.&lt;br /&gt;
&lt;br /&gt;
To create or restore a scene snapshot:&lt;br /&gt;
* Click on the camera icon (labeled &amp;quot;H&amp;quot; in the schematic above) to record a scenesnapshot. &lt;br /&gt;
* Use the pull down menu (labeled &amp;quot;L&amp;quot; in the schematic above) to select from a list of existing snapshots. &lt;br /&gt;
* Click on the arrow icon to restore the snapshot.&lt;br /&gt;
* You can also click on the trashcan icon to delete the snapshot.&lt;br /&gt;
&lt;br /&gt;
[[image:SceneSnapshots.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= Slicer Viewers = &lt;br /&gt;
In this section, Slicer's Slice Viewers and Main 3D Viewer are described, and options for configuring their layout and display of information.&lt;br /&gt;
&lt;br /&gt;
== Slice Viewers (and their Controllers) ==&lt;br /&gt;
&lt;br /&gt;
Slicer's three main Slice Viewers are color-coded Red, Yellow and Green. By default, these correspond to '''Axial''', '''Saggital''' and '''Coronal''' slice orientations respectively, but this can be modified by a user. In Slicer's '''Compare View''' layout (described a little later), the Slice Viewers are color-coded Orange.&lt;br /&gt;
&lt;br /&gt;
All Slice viewers have their own Slice Controller, which can be expanded or collapsed by clicking in the colored bar at their top, for convenience. The Red Viewer is shown below, expanded and collapsed as described. Note that corner annotations are displayed when the mouse hovers over any viewer.&lt;br /&gt;
&lt;br /&gt;
[[image:SliceControllerGUICollapseAndExpand.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Slice orientation and Oblique reformats===&lt;br /&gt;
On each Slice Viewer, an '''Orientation''' menu button in the upper left of the control panel provides the option to display an  &amp;quot;Axial&amp;quot;, &amp;quot;Coronal&amp;quot;, &amp;quot;Sagittal&amp;quot;, or &amp;quot;Reformat&amp;quot; slice orientation in the Viewer.  &lt;br /&gt;
&lt;br /&gt;
[[image:SliceGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
Slice viewers can be used to specify oblique reformats in two ways:&lt;br /&gt;
* first by using the &amp;quot;Reformat&amp;quot; orientation and CTRL-Right-Button-Move (subject to change and something of an &amp;quot;art&amp;quot; to control).&lt;br /&gt;
* and second by selecting the '''Show Reformat Widget''' option ([[image:SliceControllerShowReformatWidget.png]]) from the Slice Controller's '''More Options''' menu ([[image:SliceControllerMoreOptions.png]]), and interacting with the widget. The widget can be toggled off using the menu's '''Hide Reformat Widget''' option ([[image:SliceControllerHideReformatWidget.png]]). Using this widget's interactive box &amp;amp; arrow to reformat the slice plane (illustrated below) causes the Orientation selector to display the &amp;quot;Reformat&amp;quot; orientation, and the Slice Viewer to display the reformatted plane.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ReformatWidget.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Linking Control of Slice Viewers===&lt;br /&gt;
&lt;br /&gt;
Control of slice viewers can be linked to save time setting them up and manipulating their display individually. The icons shown below, found in the leftmost of each Slice Controller's toolbar, toggle linking and unlinking of the viewers.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-SliceLink.png]]&lt;br /&gt;
&lt;br /&gt;
When Slice Viewers are linked, the &amp;quot;linked&amp;quot; icon ([[image:AppDoc-SlicesLinked.png]])is displayed. Clicking the icon-button will unlink the Viewers, and will display the &amp;quot;Unlinked&amp;quot; icon ([[image:AppDoc-SlicesUnlinked.png]]). When the Slice Viewers are linked, many but not all of the controllers' options apply to all viewers. The following controls are linked:&lt;br /&gt;
&lt;br /&gt;
* Orientation&lt;br /&gt;
* FG, BG, Label selectors&lt;br /&gt;
* Visibility&lt;br /&gt;
* Fit To Window&lt;br /&gt;
* Adjust Label Map Opacity&lt;br /&gt;
* Show/Hide Label Volume Outlines&lt;br /&gt;
* Show/Hide Reformat Widget&lt;br /&gt;
&lt;br /&gt;
===Slice Plane Visibility in 3D Viewer===&lt;br /&gt;
&lt;br /&gt;
The Slices shown in each of the Slice Viewers may be displayed in the Main 3D Viewer as well. Their visibility in the 3D Viewer is controlled with the '''Visibility''' icon button in the Slice Controllers, as shown in the figure below. When Slices are visible in the 3D Viewer, the &amp;quot;visible&amp;quot; icon ([[image:AppDoc-SlicesVisible.png]])is displayed. Clicking the icon-button will hide the Slices in the 3D Viewer, and will display the &amp;quot;Invisible&amp;quot; icon ([[image:AppDoc-SlicesInvisible.png]]). &lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-SliceVisibility.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Other Slice GUI options===&lt;br /&gt;
&lt;br /&gt;
The Slice controllers offer other options as well, available under the '''More Options''' menubutton ([[image:SliceControllerMoreOptions.png]]). Options here include some of those available in the '''Slices Controller GUI''' and some additional. These options, each shown in the figures '''A - H''' below, include:&lt;br /&gt;
&lt;br /&gt;
* A. Fit a slice to the size of a Viewer's window&lt;br /&gt;
* B. Adjust the opacity of a label map&lt;br /&gt;
* C. Show/Hide outlines around labels in a label map&lt;br /&gt;
* D. Show/Hide the Slice Reformat Widget&lt;br /&gt;
* E. Select options for compositing slice layers&lt;br /&gt;
* F. Choose manual or automatic slice spacing modes&lt;br /&gt;
* G. Create a lightbox view within a Slice Viewer&lt;br /&gt;
* H. Adjust the display of Foreground, Background or Label layers.&lt;br /&gt;
&lt;br /&gt;
[[image:SliceGUIMoreMap.png]]&lt;br /&gt;
&lt;br /&gt;
===Configuring Slice Viewers when the Controllers are collapsed ===&lt;br /&gt;
&lt;br /&gt;
In Slicer's '''Slices Module''', all Slice Viewers' Slice Controllers are arrayed in a vertical stack; When screen real estate must be maximized, the individual Slice Viewers' Controllers can be collapsed and the GUI panel's controllers can be used to manipulate the Viewers instead. The Slices Module's GUI panel is shown below.&lt;br /&gt;
&lt;br /&gt;
[[image:SlicesGUIPanel.png |center ]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Main 3D Viewer ==&lt;br /&gt;
&lt;br /&gt;
=== Default elements and their visibility===&lt;br /&gt;
&lt;br /&gt;
Slicer's Main 3D Viewer displays a three-dimensional view of the scene. By default, the scene includes some elements for spatial reference including a 3D wireframe cube centered around the origin (0,0,0) and labels along each of the principle axes ('''R'''ight, '''L'''eft, '''S'''uperior, '''I'''nferior, '''A'''nterior, and '''P'''osterior). Slicer's default blue background color, as well as the visibility of the spatial references in the view, can be modified in the View Control GUI panel's visibility menu, as shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-VCGuiVisibility.png]]&lt;br /&gt;
&lt;br /&gt;
=== Interacting ===&lt;br /&gt;
&lt;br /&gt;
You can adjust the view in the Main 3D Viewer using the mouse or keyboard (for information on the latter, please see the Keyboard Shortcuts section):&lt;br /&gt;
&lt;br /&gt;
* '''Zoom in:''' Right-mouse-button click-and-drag toward you. (Imagine pulling the scene closer)&lt;br /&gt;
* '''Zoom out:''' Right-mouse-button click-and-drag away from you. (Imagine pushing the scene away)&lt;br /&gt;
* '''Pan''' (shift the look-at point): Middle-mouse-button click-and-drag left, right, up or down.&lt;br /&gt;
* '''Rotate Around''' a look-at point: Left-mouse-button click-and-drag.&lt;br /&gt;
&lt;br /&gt;
If you need more precise control, or if the view gets into some hard-to-manage configuration, the View Control GUI panel can be used to reset the look-from and look-at point in a manageable way:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-VCGuiSetView.png]]&lt;br /&gt;
&lt;br /&gt;
=== Window and layout configurations ===&lt;br /&gt;
&lt;br /&gt;
Slicer can be configured to show or hide the Module GUI panel, and to display it on the left or right side of the Viewers. These options are accessed as follows:&lt;br /&gt;
&lt;br /&gt;
* Show/Hide Module GUI Panel: F5-key or Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]])-&amp;gt;Toggle GUI panel visibility&lt;br /&gt;
* Move Module GUI Panel to the Left/Right: Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]])-&amp;gt;Toggle GUI panel L/R&lt;br /&gt;
* Show/Hide Bottom Panel: F6-key (this option is only really useful in Slicer's Conventional View)&lt;br /&gt;
&lt;br /&gt;
[[image:AppGUIBasicConfigure.png]]&lt;br /&gt;
&lt;br /&gt;
In addition, there are a number of ways to arrange the Slice and 3D Viewers. We hope to offer a more extensible suite of configuration options in the future. At present, these options are available from Slicer's Application Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]]), and are illustrated below:&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
&lt;br /&gt;
[[image:AppLayouts.png]]&lt;br /&gt;
&lt;br /&gt;
= Error Log =&lt;br /&gt;
&lt;br /&gt;
Finally, the application has an accessible error log in the event of unexpected behavior or error messages -- this readout is useful for reporting bugs or usability problems back to the Slicer Development Team. The error log can be raised in the following ways:&lt;br /&gt;
&lt;br /&gt;
* Typing '''Ctrl+Alt+E'''&lt;br /&gt;
* Menubar's '''Window-&amp;gt;Error Log'''&lt;br /&gt;
* Clicking the '''Error Log icon''', which is displayed only if any error reports are present, and as shown below.&lt;br /&gt;
&lt;br /&gt;
[[image:RaiseErrorLog.png]]&lt;br /&gt;
&lt;br /&gt;
[[image:ErrorLog.png]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
= Status Text and Progress Bar =&lt;br /&gt;
&lt;br /&gt;
For some operations, loading, saving or processing may take awhile; Slicer may post status text at the bottom of the Application's window (shown below) that helps you to understand what it's working on. This readout isn't available as often as it should be; we hope to address this usability issue in future software releases. If you encounter any situation in which a status update would be especially useful but none exists, please report your discovery to Slicer's bug tracker as a usability issue.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-StatusText.png  ]]&lt;br /&gt;
&lt;br /&gt;
Progress is also displayed during processing operations. One progress readout commonly used by command-line modules is found in the lower right corner of the Slicer Window in the Progress Gauge, shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ProgressBar.png |center ]]&lt;br /&gt;
&lt;br /&gt;
Some Slicer modules also use a pop-up progress dialog, which assumes &amp;quot;focus&amp;quot; and prevents you from interacting with Slicer until the processing is finished; the dialog appears as below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ProgressDialog.png |center ]]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9491</id>
		<title>Slicer3:Extensions</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9491"/>
		<updated>2009-05-08T21:13:35Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* FOR DEVELOPERS */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;3D Slicer now supports extensions.  Extensions are available from an extension server.  This allows end-users to select the extensions useful to them, without having to download the entire extension archive.&lt;br /&gt;
&lt;br /&gt;
== FOR DEVELOPERS ==&lt;br /&gt;
&lt;br /&gt;
Extensions must follow the appropriate architecture for them to be made available to end users.  See [[Slicer3::Loadable_Modules]] for an example of how to make GUI and GUI-less Loadable Modules.  Command Line and Scripted Modules will also work with this framework.&lt;br /&gt;
&lt;br /&gt;
To enable your Command Line, Scripted, or Loadable module, add an &amp;quot;s3ext&amp;quot; script to the /Slicer3/Extensions directory of the source repository:&lt;br /&gt;
&lt;br /&gt;
ExampleLoadableModule.s3ext:&lt;br /&gt;
  scm       svn&lt;br /&gt;
  svnpath   https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules/Loadable&lt;br /&gt;
  svnusername slicerbot&lt;br /&gt;
  svnpassword slicer&lt;br /&gt;
  &lt;br /&gt;
  depends&lt;br /&gt;
  &lt;br /&gt;
  homepage  http://www.nitrc.org/projects/slicer3examples/&lt;br /&gt;
  &lt;br /&gt;
  category  Examples&lt;br /&gt;
  &lt;br /&gt;
  status    Beta&lt;br /&gt;
  &lt;br /&gt;
  description An example of a loadable module using Slicer3 GUI and Logic classes, plus a MRML node.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9490</id>
		<title>Documentation/3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9490"/>
		<updated>2009-05-08T21:11:22Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Extensions for Downloading */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Note: This page is currently under construction&lt;br /&gt;
&lt;br /&gt;
=Introduction=&lt;br /&gt;
[[Image:Base-Features-and-Modules.png|thumb|right|overview|[[Media:Integrating with Slicer3.ppt | Integrating with Slicer3]]]]&lt;br /&gt;
This page is a portal for documentation about Slicer 3.4.&lt;br /&gt;
For information for software developers, please go to the Developers page (see link in navigation box to the left).&lt;br /&gt;
&lt;br /&gt;
=How-To Tutorials=&lt;br /&gt;
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]&lt;br /&gt;
&lt;br /&gt;
=Feature Request and Problem Reports=&lt;br /&gt;
We have an [http://www.na-mic.org/Bug/my_view_page.php issues tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.&lt;br /&gt;
&lt;br /&gt;
=List of Modules=&lt;br /&gt;
==Overview==&lt;br /&gt;
*The documentation on this page has been created for Slicer 3.4 and discusses the features and capabilities of menu items and panels. It is intended to be used as a live reference manual. This is a wiki. You are welcome to add to the content and improve it.&lt;br /&gt;
*In addition to the hundereds of smaller changes and improvements to Slicer in general, there are two substantial new addtions to Slicer 3.4:&lt;br /&gt;
**A new infrastructure to find and add plug-ins from a repository. See [[Documentation-3.4#Modules_for_Downloading|here]] for more information.&lt;br /&gt;
**A new database using XNAT desktop. See [[Documentation-3.4#XNAT_Desktop|here]] for more information.&lt;br /&gt;
&lt;br /&gt;
==Main GUI==&lt;br /&gt;
*[[Modules:MainApplicationGUI-Documentation-3.4| Main Application GUI]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:EventBindings-3.4| &amp;quot;Hot-keys&amp;quot; and Keyboard Shortcuts]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:DataModule-3.4| Loading Scenes and Individual Datasets through the Data Module]] (W Plesniak)&lt;br /&gt;
*[[Modules:Loading-Data-3.4| Data Loading Details]] (Steve Pieper)&lt;br /&gt;
*[[Modules:Saving-Documentation-3.4| Saving Scenes and Data]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:SceneSnapshots-3.4| Creating and Restoring Scene Snapshots]] (Alex Yarmarkovich &amp;amp; Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
==Modules==&lt;br /&gt;
*Please copy the template linked below, paste it into your page and customize it with your module's information.&lt;br /&gt;
[[Slicer3:Module_Documentation-3.4_Template|Slicer3:Module_Documentation-3.4_Template]]&lt;br /&gt;
*See above for info to be put into the Help and Acknowledgment Tabs&lt;br /&gt;
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]&lt;br /&gt;
===Core===&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)&lt;br /&gt;
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)&lt;br /&gt;
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]]  (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)&lt;br /&gt;
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)&lt;br /&gt;
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)&lt;br /&gt;
&lt;br /&gt;
Additional modules may appear in this section of the menu if they are not otherwise categorized by the developer.&lt;br /&gt;
&lt;br /&gt;
==Specialized Modules==&lt;br /&gt;
&lt;br /&gt;
Please adhere to the naming scheme for the module documentation:&lt;br /&gt;
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)&lt;br /&gt;
&lt;br /&gt;
===Wizards===&lt;br /&gt;
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)&lt;br /&gt;
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)&lt;br /&gt;
===Informatics Modules===&lt;br /&gt;
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)&lt;br /&gt;
===Registration===&lt;br /&gt;
*Overview:&lt;br /&gt;
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies. &lt;br /&gt;
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment. &lt;br /&gt;
**Linear, affine  and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output. &lt;br /&gt;
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.&lt;br /&gt;
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)&lt;br /&gt;
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)&lt;br /&gt;
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]]  (Daniel Blezek)&lt;br /&gt;
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Segmentation===&lt;br /&gt;
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)&lt;br /&gt;
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
===Statistics===&lt;br /&gt;
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Diffusion===&lt;br /&gt;
====DWI====&lt;br /&gt;
*Estimation&lt;br /&gt;
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
*Filter&lt;br /&gt;
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)&lt;br /&gt;
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)&lt;br /&gt;
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
====DTI====&lt;br /&gt;
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)&lt;br /&gt;
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)&lt;br /&gt;
*Analysis&lt;br /&gt;
&lt;br /&gt;
===Tractography===&lt;br /&gt;
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)&lt;br /&gt;
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)&lt;br /&gt;
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
===IGT===&lt;br /&gt;
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) &lt;br /&gt;
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)&lt;br /&gt;
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)&lt;br /&gt;
===Filtering===&lt;br /&gt;
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)&lt;br /&gt;
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)&lt;br /&gt;
*Arithmetic&lt;br /&gt;
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)&lt;br /&gt;
*Denoising&lt;br /&gt;
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]]  (Bill Lorensen checked this in)&lt;br /&gt;
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) &lt;br /&gt;
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)&lt;br /&gt;
*Morphology&lt;br /&gt;
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)&lt;br /&gt;
===Surface Models===&lt;br /&gt;
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)&lt;br /&gt;
*Grayscale Model Maker (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
*Freesurfer Surface Section Extraction (Katharina Quintus)&lt;br /&gt;
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Batch processing===&lt;br /&gt;
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)&lt;br /&gt;
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)&lt;br /&gt;
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)&lt;br /&gt;
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)&lt;br /&gt;
&lt;br /&gt;
===Converters===&lt;br /&gt;
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)&lt;br /&gt;
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Work in Progress===&lt;br /&gt;
Various tools in development will appear here depending on the version of slicer you are using.&lt;br /&gt;
===Developer Tools===&lt;br /&gt;
*[[Modules:PythonScript-Documentation-3.4| Python Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonNumpyScript-Documentation-3.4| Python Numpy Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExecutionModelTour-Documentation-3.4|Execution Model Tour]] (Daniel Blezek, Bill Lorensen)&lt;br /&gt;
*[[Modules:ScriptedModuleExample-Documentation-3.4| Scripted Module Example]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
=Extensions for Downloading=&lt;br /&gt;
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]&lt;br /&gt;
Work is in progress to create infrastructure for searching and loading extensions. See [[Slicer3:Extensions]] for more information.&lt;br /&gt;
*This will allow contributors and software developers to post their own Slicer extensions and have them compiled against the &amp;quot;official&amp;quot; versions of Slicer.&lt;br /&gt;
*Users can browse these contributed extensions and install them on their own versions of Slicer.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
We are currently using NITRC as a repository for contributed extensions. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.&lt;br /&gt;
Click [http://www.nitrc.org/search/?type_of_search=soft&amp;amp;words=slicer3&amp;amp;Search.x=0&amp;amp;Search.y=0&amp;amp;Search=Search  here] to see a listing of Slicer 3 extensions on NITRC.&lt;br /&gt;
&lt;br /&gt;
=XNAT Desktop and FetchMI=&lt;br /&gt;
*Work is underway to use XNAT desktop (xnd) as a local database for Slicer. This database will exist in parallel with the other load and save mechanisms and will allow to download/upload individual files or entire scenes with all their dependent files. &lt;br /&gt;
*Users of Slicer will have to install xnd on their computer. Once set up, the FetchMI interface will allow users to upload and download mrml scenes with all the dependent files, or individual volumes, models, other components of slicer scenes.&lt;br /&gt;
*See [http://nrg.wustl.edu/xnd/download here] for a link to the download site for xnd. See [http://www.xnat.org/xnd here] for documentation on how to install XNAT desktop on your computer.&lt;br /&gt;
*'''On Macs and Linux you currently have to change permissions of the executable after installation.'''&lt;br /&gt;
*In the future (summer 2009) xnd will be able to upload and download mrml scenes to xnat enterprise.&lt;br /&gt;
&lt;br /&gt;
*FetchMI is the current interface inside slicer for exploring information stored in xnd and down and upload such data. It is a &amp;quot;sandbox&amp;quot; implementation to help us understand how users will want to use remotely stored data and metadata in the Slicer environment. Eventually, FetchMI's remote load and save will be integrated with Slicer's existing load and save interfaces, and FetchMI's data tagging functionality will be more fully developed as a new metadata authoring module.&lt;br /&gt;
*See [[Modules:FetchMI-Documentation-3.4|here]] for more information about FETCHMI. User comments and suggestions are welcome.&lt;br /&gt;
&lt;br /&gt;
= Requirements for modules to be added to the release=&lt;br /&gt;
{| border=&amp;quot;00&amp;quot; cellpadding=&amp;quot;5&amp;quot; cellspacing=&amp;quot;0&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
| rowspan=&amp;quot;2&amp;quot;| &lt;br /&gt;
* The module is '''feature complete''' for the tasks advertised on 2-4-2009&lt;br /&gt;
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.&lt;br /&gt;
* Module has '''documentation''' on the [[Documentation-3.4#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.4#Modules|'''here''']] to structure your page. &lt;br /&gt;
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.&lt;br /&gt;
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.&lt;br /&gt;
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.&lt;br /&gt;
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. &lt;br /&gt;
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)&lt;br /&gt;
* If your module has [[Documentation-3.2|documentation in Slicer 3.2]], please copy/paste/update into the 3.4 version&lt;br /&gt;
| style=&amp;quot;background: #e5e5e5&amp;quot; align=&amp;quot;center&amp;quot;| Examples for the Help and &lt;br /&gt;
Acknowledgment Panels&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background: #ebeced&amp;quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] &lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9489</id>
		<title>Documentation/3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Documentation/3.4&amp;diff=9489"/>
		<updated>2009-05-08T21:11:01Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Modules for Downloading */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Note: This page is currently under construction&lt;br /&gt;
&lt;br /&gt;
=Introduction=&lt;br /&gt;
[[Image:Base-Features-and-Modules.png|thumb|right|overview|[[Media:Integrating with Slicer3.ppt | Integrating with Slicer3]]]]&lt;br /&gt;
This page is a portal for documentation about Slicer 3.4.&lt;br /&gt;
For information for software developers, please go to the Developers page (see link in navigation box to the left).&lt;br /&gt;
&lt;br /&gt;
=How-To Tutorials=&lt;br /&gt;
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]&lt;br /&gt;
&lt;br /&gt;
=Feature Request and Problem Reports=&lt;br /&gt;
We have an [http://www.na-mic.org/Bug/my_view_page.php issues tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.&lt;br /&gt;
&lt;br /&gt;
=List of Modules=&lt;br /&gt;
==Overview==&lt;br /&gt;
*The documentation on this page has been created for Slicer 3.4 and discusses the features and capabilities of menu items and panels. It is intended to be used as a live reference manual. This is a wiki. You are welcome to add to the content and improve it.&lt;br /&gt;
*In addition to the hundereds of smaller changes and improvements to Slicer in general, there are two substantial new addtions to Slicer 3.4:&lt;br /&gt;
**A new infrastructure to find and add plug-ins from a repository. See [[Documentation-3.4#Modules_for_Downloading|here]] for more information.&lt;br /&gt;
**A new database using XNAT desktop. See [[Documentation-3.4#XNAT_Desktop|here]] for more information.&lt;br /&gt;
&lt;br /&gt;
==Main GUI==&lt;br /&gt;
*[[Modules:MainApplicationGUI-Documentation-3.4| Main Application GUI]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:EventBindings-3.4| &amp;quot;Hot-keys&amp;quot; and Keyboard Shortcuts]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:DataModule-3.4| Loading Scenes and Individual Datasets through the Data Module]] (W Plesniak)&lt;br /&gt;
*[[Modules:Loading-Data-3.4| Data Loading Details]] (Steve Pieper)&lt;br /&gt;
*[[Modules:Saving-Documentation-3.4| Saving Scenes and Data]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:SceneSnapshots-3.4| Creating and Restoring Scene Snapshots]] (Alex Yarmarkovich &amp;amp; Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
==Modules==&lt;br /&gt;
*Please copy the template linked below, paste it into your page and customize it with your module's information.&lt;br /&gt;
[[Slicer3:Module_Documentation-3.4_Template|Slicer3:Module_Documentation-3.4_Template]]&lt;br /&gt;
*See above for info to be put into the Help and Acknowledgment Tabs&lt;br /&gt;
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]&lt;br /&gt;
===Core===&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)&lt;br /&gt;
&lt;br /&gt;
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)&lt;br /&gt;
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)&lt;br /&gt;
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]]  (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)&lt;br /&gt;
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)&lt;br /&gt;
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)&lt;br /&gt;
&lt;br /&gt;
Additional modules may appear in this section of the menu if they are not otherwise categorized by the developer.&lt;br /&gt;
&lt;br /&gt;
==Specialized Modules==&lt;br /&gt;
&lt;br /&gt;
Please adhere to the naming scheme for the module documentation:&lt;br /&gt;
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)&lt;br /&gt;
&lt;br /&gt;
===Wizards===&lt;br /&gt;
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)&lt;br /&gt;
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)&lt;br /&gt;
===Informatics Modules===&lt;br /&gt;
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)&lt;br /&gt;
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)&lt;br /&gt;
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)&lt;br /&gt;
===Registration===&lt;br /&gt;
*Overview:&lt;br /&gt;
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies. &lt;br /&gt;
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment. &lt;br /&gt;
**Linear, affine  and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output. &lt;br /&gt;
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.&lt;br /&gt;
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)&lt;br /&gt;
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)&lt;br /&gt;
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]]  (Daniel Blezek)&lt;br /&gt;
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Segmentation===&lt;br /&gt;
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)&lt;br /&gt;
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)&lt;br /&gt;
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
===Statistics===&lt;br /&gt;
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Diffusion===&lt;br /&gt;
====DWI====&lt;br /&gt;
*Estimation&lt;br /&gt;
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
*Filter&lt;br /&gt;
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)&lt;br /&gt;
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja Fernandez)&lt;br /&gt;
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)&lt;br /&gt;
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
====DTI====&lt;br /&gt;
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)&lt;br /&gt;
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)&lt;br /&gt;
*Analysis&lt;br /&gt;
&lt;br /&gt;
===Tractography===&lt;br /&gt;
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)&lt;br /&gt;
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)&lt;br /&gt;
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)&lt;br /&gt;
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)&lt;br /&gt;
&lt;br /&gt;
===IGT===&lt;br /&gt;
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) &lt;br /&gt;
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)&lt;br /&gt;
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)&lt;br /&gt;
===Filtering===&lt;br /&gt;
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)&lt;br /&gt;
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)&lt;br /&gt;
*Arithmetic&lt;br /&gt;
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)&lt;br /&gt;
*Denoising&lt;br /&gt;
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]]  (Bill Lorensen checked this in)&lt;br /&gt;
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) &lt;br /&gt;
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)&lt;br /&gt;
*Morphology&lt;br /&gt;
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)&lt;br /&gt;
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)&lt;br /&gt;
===Surface Models===&lt;br /&gt;
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)&lt;br /&gt;
*Grayscale Model Maker (Bill Lorensen)&lt;br /&gt;
&lt;br /&gt;
*Freesurfer Surface Section Extraction (Katharina Quintus)&lt;br /&gt;
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)&lt;br /&gt;
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)&lt;br /&gt;
&lt;br /&gt;
===Batch processing===&lt;br /&gt;
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)&lt;br /&gt;
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)&lt;br /&gt;
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)&lt;br /&gt;
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)&lt;br /&gt;
&lt;br /&gt;
===Converters===&lt;br /&gt;
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)&lt;br /&gt;
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)&lt;br /&gt;
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
===Work in Progress===&lt;br /&gt;
Various tools in development will appear here depending on the version of slicer you are using.&lt;br /&gt;
===Developer Tools===&lt;br /&gt;
*[[Modules:PythonScript-Documentation-3.4| Python Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:PythonNumpyScript-Documentation-3.4| Python Numpy Script]] (Luca Antiga, Daniel Blezek)&lt;br /&gt;
*[[Modules:ExecutionModelTour-Documentation-3.4|Execution Model Tour]] (Daniel Blezek, Bill Lorensen)&lt;br /&gt;
*[[Modules:ScriptedModuleExample-Documentation-3.4| Scripted Module Example]] (Steve Pieper)&lt;br /&gt;
&lt;br /&gt;
=Extensions for Downloading=&lt;br /&gt;
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]&lt;br /&gt;
Work is in progress to create infrastructure for searching and loading extensions. See [[Slicer3:Extensions]] for more information.&lt;br /&gt;
*This will allow contributors and software developers to post their own Slicer extensions and have them compiled against the &amp;quot;official&amp;quot; versions of Slicer.&lt;br /&gt;
*Users can browse these contributed extensions and install them on their own versions of Slicer.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
We are currently using NITRC as a repository for contributed extensions. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.&lt;br /&gt;
Click [http://www.nitrc.org/search/?type_of_search=soft&amp;amp;words=slicer3&amp;amp;Search.x=0&amp;amp;Search.y=0&amp;amp;Search=Search  here] to see a listing of Slicer 3 modules on NITRC.&lt;br /&gt;
&lt;br /&gt;
=XNAT Desktop and FetchMI=&lt;br /&gt;
*Work is underway to use XNAT desktop (xnd) as a local database for Slicer. This database will exist in parallel with the other load and save mechanisms and will allow to download/upload individual files or entire scenes with all their dependent files. &lt;br /&gt;
*Users of Slicer will have to install xnd on their computer. Once set up, the FetchMI interface will allow users to upload and download mrml scenes with all the dependent files, or individual volumes, models, other components of slicer scenes.&lt;br /&gt;
*See [http://nrg.wustl.edu/xnd/download here] for a link to the download site for xnd. See [http://www.xnat.org/xnd here] for documentation on how to install XNAT desktop on your computer.&lt;br /&gt;
*'''On Macs and Linux you currently have to change permissions of the executable after installation.'''&lt;br /&gt;
*In the future (summer 2009) xnd will be able to upload and download mrml scenes to xnat enterprise.&lt;br /&gt;
&lt;br /&gt;
*FetchMI is the current interface inside slicer for exploring information stored in xnd and down and upload such data. It is a &amp;quot;sandbox&amp;quot; implementation to help us understand how users will want to use remotely stored data and metadata in the Slicer environment. Eventually, FetchMI's remote load and save will be integrated with Slicer's existing load and save interfaces, and FetchMI's data tagging functionality will be more fully developed as a new metadata authoring module.&lt;br /&gt;
*See [[Modules:FetchMI-Documentation-3.4|here]] for more information about FETCHMI. User comments and suggestions are welcome.&lt;br /&gt;
&lt;br /&gt;
= Requirements for modules to be added to the release=&lt;br /&gt;
{| border=&amp;quot;00&amp;quot; cellpadding=&amp;quot;5&amp;quot; cellspacing=&amp;quot;0&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
| rowspan=&amp;quot;2&amp;quot;| &lt;br /&gt;
* The module is '''feature complete''' for the tasks advertised on 2-4-2009&lt;br /&gt;
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.&lt;br /&gt;
* Module has '''documentation''' on the [[Documentation-3.4#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.4#Modules|'''here''']] to structure your page. &lt;br /&gt;
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.&lt;br /&gt;
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.&lt;br /&gt;
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.&lt;br /&gt;
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. &lt;br /&gt;
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)&lt;br /&gt;
* If your module has [[Documentation-3.2|documentation in Slicer 3.2]], please copy/paste/update into the 3.4 version&lt;br /&gt;
| style=&amp;quot;background: #e5e5e5&amp;quot; align=&amp;quot;center&amp;quot;| Examples for the Help and &lt;br /&gt;
Acknowledgment Panels&lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;background: #ebeced&amp;quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] &lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Modules:MainApplicationGUI-Documentation-3.4&amp;diff=9488</id>
		<title>Modules:MainApplicationGUI-Documentation-3.4</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Modules:MainApplicationGUI-Documentation-3.4&amp;diff=9488"/>
		<updated>2009-05-08T20:59:58Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* View menu */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[Documentation-3.4#Main_GUI|Return to Slicer Documentation]]&lt;br /&gt;
&lt;br /&gt;
'''Overview'''&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Slicer3's main desktop interface provides top-level access to most commonly-used features, and organizes them into logical groupings. These groups of features are presented in a number of interface panels on the GUI, as is illustrated in the basic layout below. The interface is designed to be easy to learn and remember, to ease navigation of Slicer's large (and growing) functionality, and to easily collapse and hide when you don't need to see it. Figures A through I in the &amp;quot;Individual frames&amp;quot; gallery a little further down on this page provide richer detail and will be described in the following sections.&lt;br /&gt;
&lt;br /&gt;
[[image:SlicerGUIIntro.png ]]&lt;br /&gt;
&lt;br /&gt;
As shown above, the logical groupings of Slicer's interface elements include:&lt;br /&gt;
* The Application Menubar&lt;br /&gt;
* The Application Toolbar&lt;br /&gt;
* The Main GUI Panel, which consists of:&lt;br /&gt;
** Slicer's Logo Panel&lt;br /&gt;
** The Module GUI Panel&lt;br /&gt;
** The Slice Viewer Controls&lt;br /&gt;
** The 3D Viewer Controls&lt;br /&gt;
* The 3D Viewer&lt;br /&gt;
* Three Main Slice Viewers (Red, Yellow, and Green)and additional Slice Viewers&lt;br /&gt;
* The Message Bar and Progress Gauge&lt;br /&gt;
* And the Error Log Button&lt;br /&gt;
&lt;br /&gt;
An overview of the functionality provided in each of these interface elements is provided below.&lt;br /&gt;
&lt;br /&gt;
=Individual Panels=&lt;br /&gt;
&lt;br /&gt;
&amp;lt;gallery perrow=&amp;quot;3&amp;quot; widths=&amp;quot;300px&amp;quot; heights=&amp;quot;200px&amp;quot;&amp;gt;&lt;br /&gt;
Image:AppGUIMap.png | '''Figure A.''' Schematic of the [[ Modules:MainApplicationGUI-Documentation-3.2#Main_Application_GUI_organization | main application GUI ]]&lt;br /&gt;
Image:AppToolbarMap.png | '''Figure B.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#Application_Toolbar | Application Toolbar ]]&lt;br /&gt;
Image:SCGUIMap.png | '''Figure C.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewer_Control_Panel | Controller for all Slice Viewers ]]&lt;br /&gt;
Image:VCGUIMap.png | '''Figure D.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#3D_Viewer_Control_Panel | Controller for the 3D Viewer ]]&lt;br /&gt;
image:SliceGUIMap.png | '''Figure E.''' Schematic of a [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewers_.26_Controllers | Slice Viewer and Slice Controller]]&lt;br /&gt;
Image:ModuleGUIPanel.png | '''Figure F.''' Schematic of an [[Modules:MainApplicationGUI-Documentation-3.4#Module_GUI_Panel | expanding/collapsing module GUI panel ]]&lt;br /&gt;
Image:SliceGUIMoreMap.png | '''Figure G.''' Schematic of [[Modules:MainApplicationGUI-Documentation-3.2#Slice_Viewers_.26_Controllers | Slice Viewer additional options ]]&lt;br /&gt;
Image:AppSettingsGUIMap.png | '''Figure H.''' Schematics of the [[Modules:MainApplicationGUI-Documentation-3.2#View-.3EApplication_Settings_Interface: | Application Settings Interface ]]&lt;br /&gt;
Image:RemoteIOGUIMap.png | '''Figure I.''' Schematic of the [[Modules:MainApplicationGUI-Documentation-3.2#View-.3ECache_.26_RemoteIO_Manager: | Remote Data Handling Interface ]]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Application Menubar =&lt;br /&gt;
The Application menubar is at the very top of Slicer3's main window, as noted above and in Figure A. Its menus and functionality are briefly listed below.&lt;br /&gt;
&lt;br /&gt;
== File menu ==&lt;br /&gt;
&lt;br /&gt;
Several loading options are available from the file menu. Below is a '''general overview''' of these options. For more details and suggestions for common use cases, see [[ Modules:Loading-Data-3.4 | Data loading details for Slicer3.4]]. For information about accessing the functionality described below and loading other types of data (like transforms, fiducial lists, color tables, DTI fiber bundles ''etc''.) through the Data Module, see [[Modules:DataModule-3.4 | Slicer's Data Module documentation]].&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Load Scene:''' &lt;br /&gt;
&lt;br /&gt;
This command raises a file browser (shown below). Slicer's file browser has a 'favorites' icon that allows you to save often-visited directories on the browser's left panel. Other features, including icons that allow you to navigate your browsing history, pop up a level in the directory structure (or folder hierarchy) and create new folders. To load a scene, navigate to a file of the appropriate format (.mrml, .xcat (XCEDE catalog file), or .xml (Slicer2 scene file) and select it for loading into Slicer. '''The command first clears any existing scene''' in Slicer and '''resets the application state'''.&lt;br /&gt;
&lt;br /&gt;
[[image:FileBrowser.png]]&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Import Scene:'''&lt;br /&gt;
&lt;br /&gt;
This command raises the same file browser shown above. Navigate to and select a scene file to be added to the existing Slicer scene. '''(The existing scene is not cleared)'''.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Add Data:'''&lt;br /&gt;
&lt;br /&gt;
This command raises an &amp;quot;Add Data&amp;quot; widget (shown below) that allows you to select individual datasets to add to the existing scene. This load option is most useful when you want to load many different data types at once (volumes, models, ''etc.'') which may not yet be described by a scene file. It exposes the following functionality:&lt;br /&gt;
&lt;br /&gt;
* The &amp;quot;Add Directory&amp;quot; button adds all files within the selected directory to the file list.&lt;br /&gt;
* The &amp;quot;Add File(s)&amp;quot; button adds all selected files to the file list.&lt;br /&gt;
* The array of buttons across the top allow you to select and deselect files in the file list, remove selected files from the list, or describe how files should be loaded.&lt;br /&gt;
* The &amp;quot;Apply&amp;quot; button loads all datasets in the list, and&lt;br /&gt;
* The &amp;quot;Cancel&amp;quot; button aborts the entire load.&lt;br /&gt;
&lt;br /&gt;
[[image:AppAddData.png]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Add Volume:''' &lt;br /&gt;
&lt;br /&gt;
This command raises an &amp;quot;Add Volume&amp;quot; widget (shown below) that allows you to select a volumetric dataset to add to the existing scene. The &amp;quot;Volume Options&amp;quot; panel can be used to clarify how a selected dataset should be loaded and displayed. This load option is particularly useful for loading DICOM data, for which its DICOM information parsing panel can be helpful.&lt;br /&gt;
&lt;br /&gt;
[[image:AppAddVolume.png]]&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Save:'''&lt;br /&gt;
&lt;br /&gt;
This command displays the &amp;quot;Save Data&amp;quot; widget, which offers many options for saving a scene and/or individual datasets. The widget is shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppSaveData.png]]&lt;br /&gt;
&lt;br /&gt;
'''Specifying a scene file to save:''' The ''Scene Description'' entry is always listed in the top row of the table. If a scene has already been loaded from a MRML file, then its filename is presented as the default choice. To save the scene into a '''new''' MRML file, either provide an alternate file name, or provide a new Data Directory.  &lt;br /&gt;
&lt;br /&gt;
'''Indicating new and unsaved datasets:''' When the panel is first displayed, all datasets which have been newly created or modified since the scene was saved are checked by default in the ''Save'' column. Any datasets in the scene can be checked/unchecked for saving/not saving using the checkboxes provided in this column. The icon buttons in the top left corner (from left to right) of the window provide shortcuts to modify the default selection:&lt;br /&gt;
&lt;br /&gt;
* '''Select Scene and Modified Data''', &lt;br /&gt;
* '''Select Modified Data'''only,&lt;br /&gt;
* '''Select All''', and&lt;br /&gt;
* '''Select None'''.&lt;br /&gt;
&lt;br /&gt;
These icons are shown and annotated below, under the SaveData illustration. Any individual checkbox can also be used to modify the selection state.  &lt;br /&gt;
&lt;br /&gt;
[[image:AppSaveDataIcons.png]]&lt;br /&gt;
&lt;br /&gt;
'''Converting to other data formats:''' Any dataset can be converted to a different (supported) format by editing the filename extension. '''Note that some format conversions may be lossy'''. To change formats, select from the list provided in the File Format column. A dataset's filepath and filename may be edited to save the dataset in a location different from that specified. &lt;br /&gt;
&lt;br /&gt;
'''Supported formats:''' Formats that can be saved include:&lt;br /&gt;
* Volumes&lt;br /&gt;
** NRRD (.nrrd)&lt;br /&gt;
** NRRD (.nhdr)&lt;br /&gt;
** MetaImage (.mhd)&lt;br /&gt;
** MetaImage (.mha)&lt;br /&gt;
** VTK (.vtk)&lt;br /&gt;
** Analyze (.hdr)&lt;br /&gt;
** Analyze (.img)&lt;br /&gt;
** Analyze (.img.gz)&lt;br /&gt;
** BMP (.bmp, .BMP)&lt;br /&gt;
** BioRad (.pic)&lt;br /&gt;
** Brains2 (.mask)&lt;br /&gt;
** GIPL (.gipl, .gipl.gz)&lt;br /&gt;
** JPEG (.jpg, .jpeg, .JPG, .JPEG)&lt;br /&gt;
** LSM (.lms, .LSM)&lt;br /&gt;
** NifTI (.nia)&lt;br /&gt;
** NifTI (.nii, .nii.gz)&lt;br /&gt;
** PNG (.png, .PNG)&lt;br /&gt;
** Stimulate (.spr)&lt;br /&gt;
** TIFF (.tiff, .tif, .TIFF, .TIF)&lt;br /&gt;
* Models&lt;br /&gt;
** Poly Data (.vtk)&lt;br /&gt;
** XML Poly Data (.vtp)&lt;br /&gt;
** STL (.stl)&lt;br /&gt;
* Fiducials&lt;br /&gt;
** Fiducial List CSV (.fcsv)&lt;br /&gt;
** Text (.txt)&lt;br /&gt;
* Transforms&lt;br /&gt;
** Transform (.tfm)&lt;br /&gt;
** Text (.txt)&lt;br /&gt;
&lt;br /&gt;
'''Saving data:''' Finally, selecting the ''Save Selected'' button will launch the scene/data saving process, and ''Cancel'' will abort it.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Close Scene:''' &lt;br /&gt;
&lt;br /&gt;
This command closes the current scene and resets the application state.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''File-&amp;gt;Exit'''&lt;br /&gt;
&lt;br /&gt;
This command exits Slicer.&lt;br /&gt;
&lt;br /&gt;
== Edit menu ==&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Set Home'''&lt;br /&gt;
&lt;br /&gt;
This command sets a user's 'home module', which is the module displayed by default each time the Slicer application is started. The home module is saved in the Application Registry.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Undo''' &lt;br /&gt;
&lt;br /&gt;
This command undoes the history of undoable commands, from last to first. &lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Redo''' &lt;br /&gt;
&lt;br /&gt;
This command re-does the history of commands most recently undone, from last to first.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;Edit Box''' &lt;br /&gt;
&lt;br /&gt;
This command raises the Edit-box, a lightweight image editing tool.&lt;br /&gt;
&lt;br /&gt;
'''Edit-&amp;gt;New Fiducial List'''&lt;br /&gt;
 &lt;br /&gt;
This command creates a new list of fiducial points.&lt;br /&gt;
&lt;br /&gt;
==View menu ==&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Manage Extensions:'''&lt;br /&gt;
&lt;br /&gt;
This Extensions Management Wizard provides status and information about available extensions for 3.4&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Cache &amp;amp; RemoteIO Manager:'''&lt;br /&gt;
&lt;br /&gt;
The Cache and Remote Data Handling interface provides status and information about all remote data transfers, and allows some control over the local cache. Remote I/O and Cache preferences can also be set in the Application Settings Interface, described next. Whether you set preferences here or there, they are saved in the Application Registry so that your settings are preserved each time you start up the Slicer Application.&lt;br /&gt;
&lt;br /&gt;
The pop-up interface is shown below. Checkbuttons at the top left provide choices about download and caching behavior, and the cache directory, cache size limit, and cache free space buffer can be set at the interface bottom. Icon buttons at the top right allow global operations on all data transfers (cache clearing and transfer cancellation) and display updates (transfer panel cleanup and cache report refreshing). Each data transfer is listed in the transfer panel along with some information about its type and status. &lt;br /&gt;
&lt;br /&gt;
[[image:RemoteIOGUIMap.png]]&lt;br /&gt;
&lt;br /&gt;
Below, all of the Cache &amp;amp; Remote Data I/O Manager icons are listed and described:&lt;br /&gt;
&lt;br /&gt;
[[image:RemoteIOIcons.png |center ]]&lt;br /&gt;
&lt;br /&gt;
'''View-&amp;gt;Application Settings Interface:'''&lt;br /&gt;
&lt;br /&gt;
The Application Settings interface provides options for saving many of Slicer's Interface and Remote Data Handling options to the Application Registry, so they are preserved across sessions. The first time you start the application, it is recommended that you browse these settings and select options that you prefer. Some of the options provided in the interface are listed below:&lt;br /&gt;
&lt;br /&gt;
* ''Slicer Settings'' allow you to specify whether Slicer should confirm on delete, and set the location for other applications that Slicer may need to use (Firefox, Zip, ''etc.''). &lt;br /&gt;
* ''Font Settings'' options allows you to choose among several fonts and relative font sizes to be displayed in the GUI.&lt;br /&gt;
* ''Module Settings'' options allow you to select a Temporary directory, a home module (that will be displayed each time Slicer starts up) and whether Slicer should include loadable and command-line modules on startup.&lt;br /&gt;
* ''Remote Data Handling Settings'' options allow the specification of Cache and Remote Data I/O settings which are also configurable from the Cache and Remote Data I/O Manager described above.&lt;br /&gt;
&lt;br /&gt;
[[image:AppSettingsGUIMap.png]]&lt;br /&gt;
&lt;br /&gt;
==Window menu ==&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Hide/Show Main Panel (Hotkey = F5):'''&lt;br /&gt;
 &lt;br /&gt;
This command collapses or expands the GUI panel and allows Slicer's viewers to occupy the entire application window, as shown below in Application Layouts figure C.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Hide/Show Bottom Panel (Hotkey = F6):'''&lt;br /&gt;
 &lt;br /&gt;
This command collapses or expands the bottom split-panel in which Slice viewers are conventionally displayed, allowing the 3D view to occupy the vertical extent of the application window. The behavior of this command will vary, and may not be appropriate, depending on the selected layout (-- available layouts are described below.)&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Toolbars:'''&lt;br /&gt;
&lt;br /&gt;
This command allows hiding or exposing sub-toolbars in the application toolbars, including the Load/Save toolbar, the undo/redo toolbar, the layout configuration, and the mouse mode toolbar.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Log Window (Hotkey = Ctrl+Alt+E):'''&lt;br /&gt;
&lt;br /&gt;
This command raises the error log display.&lt;br /&gt;
&lt;br /&gt;
'''Window-&amp;gt;Tcl Interactor (Hotkey = Ctrl+T):'''&lt;br /&gt;
 &lt;br /&gt;
This command raises the Tcl interactor for scripted interaction with Slicer data:&lt;br /&gt;
&lt;br /&gt;
[[image:TclInteractor.png |center ]]&lt;br /&gt;
&lt;br /&gt;
==Help menu ==&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;Browse Tutorials:'''&lt;br /&gt;
&lt;br /&gt;
Raises Slicer's training page in mozilla firefox web browser (Note: you will need to have specified the location of Mozilla Firefox executable in Slicer's Application Settings Interface: '''Application Settings-&amp;gt;Slicer Settings''').&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;About Slicer3:'''&lt;br /&gt;
&lt;br /&gt;
Provides a description of the Slicer3 effort and its support.&lt;br /&gt;
&lt;br /&gt;
'''Help-&amp;gt;Keyboard Shortcuts:'''&lt;br /&gt;
&lt;br /&gt;
Raises a window that lists commonly-used keyboard shortcuts.&lt;br /&gt;
&lt;br /&gt;
==Feedback menu ==&lt;br /&gt;
'''Note: for all commands in the Feedback Menu, you will need to have specified the location of your Mozilla Firefox executable in Slicer's Application Settings Interface: Application Settings-&amp;gt;Slicer Settings) so Slicer knows how to launch the web browser.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Report a Bug:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that any bug you encounter can quickly and easily be reported. Be sure to select the appropriate category for the bug and estimate its severity. It's recommended that you provide as much information as you can so that the bug can be reproduced by the development team.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Report a Usability Issue:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that any usability issue you encounter can quickly be captured. Be sure to select the &amp;quot;usability&amp;quot; category for the issue and estimate its severity. We request that you describe the way in which the usability issue is impacting your work so that the usability and development team can address the issue appropriately. Suggestions and ideas are welcome!&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Make a Feature Request:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.na-mic.org/Bug/my_view_page.php so that community feature requests can easily be collected. We request that you clearly mark your submission as a &amp;quot;feature request&amp;quot; in the description field of the form.&lt;br /&gt;
&lt;br /&gt;
'''Feedback-&amp;gt;Community:'''&lt;br /&gt;
 &lt;br /&gt;
This command opens your Firefox web browser to http://www.slicer.org/slicerWiki/index.php/Slicer3:VisualBlog where you can post screenshots of interesting ways you are using the Slicer3 software package in your research and share them with the Slicer community.&lt;br /&gt;
&lt;br /&gt;
= Application Toolbar =&lt;br /&gt;
&lt;br /&gt;
Slicer's toolbar provides quick access to centralized load / save functionality, options for searching for and navigating among modules, undo/redo capability, ability to select different application layouts and change among mouse modes. Using and indicating mouse modes in Slicer is still under development, so this part of the toolbar will likely change in future releases. For now, &amp;quot;Mouse place&amp;quot; is used to create new objects, like fiducial points. &amp;quot;Mouse pick&amp;quot; is intended for selecting objects. &amp;quot;Transform view&amp;quot; is the default mode, used to pan, zoom and rotate the camera in the 3D viewer. Individual icons in the toolbar are labeled below.&lt;br /&gt;
&lt;br /&gt;
[[image:AppToolbarMap.png]]&lt;br /&gt;
&lt;br /&gt;
The Window-&amp;gt;Toolbars submenu allows showing/hiding parts of this toolbar, including the Load/Save toolbar, the undo/redo toolbar, the layout configuration, and the mouse mode toolbar.&lt;br /&gt;
&lt;br /&gt;
= Module GUI Panel =&lt;br /&gt;
&lt;br /&gt;
=='''Conventions and window position:'''==&lt;br /&gt;
By default, the Module GUI panel is located on the left of the application window. The panel that contains the Module GUI, Slices Control GUI and 3D Viewer Control GUI (both described below) can be moved to the right side also by selecting that option from the layout menu on the toolbar, if that working configuration is found to be more convenient. Each Slicer module populates the Module GUI panel with its interface; all modules have a Help &amp;amp; Acknowledgement frame that presents brief help text and pointers to additional information, and appropriate acknowledgement for the work as shown in the figure below. &lt;br /&gt;
&lt;br /&gt;
=='''Collapsing and expanding frames:'''==&lt;br /&gt;
Each module GUI contains its functionality inside collapsing and expanding frames, also shown below, to minimize the need to scroll among individual blocks of functionality within a module. The frames can be collapsed or expanded by clicking in the title frame. The Slices Control and 3D Viewer Control GUI panels also can be collapsed to make more space for a module GUI. &lt;br /&gt;
&lt;br /&gt;
Brief '''Help Text''' and '''Module Attribution and Acknowledgements''' can be found in the topmost panel in any module.&lt;br /&gt;
&lt;br /&gt;
[[image:ModuleGUIPanel.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= Slice Viewer Control Panel =&lt;br /&gt;
The Slice Viewer Control Panel allows configuration of all Slice GUIs at once. The functionality represented by icons in Slicer Version 3.2 is described below:&lt;br /&gt;
&lt;br /&gt;
[[image:SCGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= 3D Viewer Control Panel =&lt;br /&gt;
&lt;br /&gt;
The 3D Viewer Control Panel provides many options for configuring the 3D viewer. The left-most panel allows the view to be oriented along any of the six principle axes ('''S'''uperior, '''I'''nferor, '''A'''nterior, '''P'''osterior, '''L'''eft or '''R'''ight). Axis symbols highlight on mouse-over. The functionality included in the panel represented by icons and checkboxes is described in the diagram below. Finally, the rightmost viewer duals as a birds-eye-view display of the entire scene, or a slice magnifier window when the mouse moves over any of the slice windows.&lt;br /&gt;
&lt;br /&gt;
[[image:VCGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
== Stereoscopic and Kinetic Depth ==&lt;br /&gt;
The 3D Viewer provides a number of options for assessing depth and layout in complicated scenes. The stereo viewing pull-down menu, labeled &amp;quot;M&amp;quot; in the schmatic above, provides several stereo viewing options, and the view rock (labeled &amp;quot;O&amp;quot;) and view spin (labeled &amp;quot;N&amp;quot;) animate the scene to help clarify feature shape, depth and layout.&lt;br /&gt;
&lt;br /&gt;
== Screen Captures (&amp;quot;Screenshots&amp;quot;)==&lt;br /&gt;
Screen captures of the 3D Viewer can be saved by selecting the icon labeled &amp;quot;D&amp;quot; in the schematic above. This raises the Screen Capture interface (shown below) that allows you to specify a save destination, a filename, version number, image format and exposes the option for overwriting existing files.&lt;br /&gt;
&lt;br /&gt;
[[image:VCGUI-Screenshots.png |center ]]&lt;br /&gt;
&lt;br /&gt;
== Scene Snapshots==&lt;br /&gt;
Scene snapshots provide a way to record particular compositions of a scene. These compositions are saved with the scene and can be restored for later inspection. Among the things recorded in each snapshot are: &lt;br /&gt;
* Model visibility,&lt;br /&gt;
* Volume display threshold, window and level settings, &lt;br /&gt;
* Slice visibility in the 3D view.&lt;br /&gt;
&lt;br /&gt;
To create or restore a scene snapshot:&lt;br /&gt;
* Click on the camera icon (labeled &amp;quot;H&amp;quot; in the schematic above) to record a scenesnapshot. &lt;br /&gt;
* Use the pull down menu (labeled &amp;quot;L&amp;quot; in the schematic above) to select from a list of existing snapshots. &lt;br /&gt;
* Click on the arrow icon to restore the snapshot.&lt;br /&gt;
* You can also click on the trashcan icon to delete the snapshot.&lt;br /&gt;
&lt;br /&gt;
[[image:SceneSnapshots.png |center ]]&lt;br /&gt;
&lt;br /&gt;
= Slicer Viewers = &lt;br /&gt;
In this section, Slicer's Slice Viewers and Main 3D Viewer are described, and options for configuring their layout and display of information.&lt;br /&gt;
&lt;br /&gt;
== Slice Viewers (and their Controllers) ==&lt;br /&gt;
&lt;br /&gt;
Slicer's three main Slice Viewers are color-coded Red, Yellow and Green. By default, these correspond to '''Axial''', '''Saggital''' and '''Coronal''' slice orientations respectively, but this can be modified by a user. In Slicer's '''Compare View''' layout (described a little later), the Slice Viewers are color-coded Orange.&lt;br /&gt;
&lt;br /&gt;
All Slice viewers have their own Slice Controller, which can be expanded or collapsed by clicking in the colored bar at their top, for convenience. The Red Viewer is shown below, expanded and collapsed as described. Note that corner annotations are displayed when the mouse hovers over any viewer.&lt;br /&gt;
&lt;br /&gt;
[[image:SliceControllerGUICollapseAndExpand.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Slice orientation and Oblique reformats===&lt;br /&gt;
On each Slice Viewer, an '''Orientation''' menu button in the upper left of the control panel provides the option to display an  &amp;quot;Axial&amp;quot;, &amp;quot;Coronal&amp;quot;, &amp;quot;Sagittal&amp;quot;, or &amp;quot;Reformat&amp;quot; slice orientation in the Viewer.  &lt;br /&gt;
&lt;br /&gt;
[[image:SliceGUIMap.png |center ]]&lt;br /&gt;
&lt;br /&gt;
Slice viewers can be used to specify oblique reformats in two ways:&lt;br /&gt;
* first by using the &amp;quot;Reformat&amp;quot; orientation and CTRL-Right-Button-Move (subject to change and something of an &amp;quot;art&amp;quot; to control).&lt;br /&gt;
* and second by selecting the '''Show Reformat Widget''' option ([[image:SliceControllerShowReformatWidget.png]]) from the Slice Controller's '''More Options''' menu ([[image:SliceControllerMoreOptions.png]]), and interacting with the widget. The widget can be toggled off using the menu's '''Hide Reformat Widget''' option ([[image:SliceControllerHideReformatWidget.png]]). Using this widget's interactive box &amp;amp; arrow to reformat the slice plane (illustrated below) causes the Orientation selector to display the &amp;quot;Reformat&amp;quot; orientation, and the Slice Viewer to display the reformatted plane.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ReformatWidget.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Linking Control of Slice Viewers===&lt;br /&gt;
&lt;br /&gt;
Control of slice viewers can be linked to save time setting them up and manipulating their display individually. The icons shown below, found in the leftmost of each Slice Controller's toolbar, toggle linking and unlinking of the viewers.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-SliceLink.png]]&lt;br /&gt;
&lt;br /&gt;
When Slice Viewers are linked, the &amp;quot;linked&amp;quot; icon ([[image:AppDoc-SlicesLinked.png]])is displayed. Clicking the icon-button will unlink the Viewers, and will display the &amp;quot;Unlinked&amp;quot; icon ([[image:AppDoc-SlicesUnlinked.png]]). When the Slice Viewers are linked, many but not all of the controllers' options apply to all viewers. The following controls are linked:&lt;br /&gt;
&lt;br /&gt;
* Orientation&lt;br /&gt;
* FG, BG, Label selectors&lt;br /&gt;
* Visibility&lt;br /&gt;
* Fit To Window&lt;br /&gt;
* Adjust Label Map Opacity&lt;br /&gt;
* Show/Hide Label Volume Outlines&lt;br /&gt;
* Show/Hide Reformat Widget&lt;br /&gt;
&lt;br /&gt;
===Slice Plane Visibility in 3D Viewer===&lt;br /&gt;
&lt;br /&gt;
The Slices shown in each of the Slice Viewers may be displayed in the Main 3D Viewer as well. Their visibility in the 3D Viewer is controlled with the '''Visibility''' icon button in the Slice Controllers, as shown in the figure below. When Slices are visible in the 3D Viewer, the &amp;quot;visible&amp;quot; icon ([[image:AppDoc-SlicesVisible.png]])is displayed. Clicking the icon-button will hide the Slices in the 3D Viewer, and will display the &amp;quot;Invisible&amp;quot; icon ([[image:AppDoc-SlicesInvisible.png]]). &lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-SliceVisibility.png |center ]]&lt;br /&gt;
&lt;br /&gt;
===Other Slice GUI options===&lt;br /&gt;
&lt;br /&gt;
The Slice controllers offer other options as well, available under the '''More Options''' menubutton ([[image:SliceControllerMoreOptions.png]]). Options here include some of those available in the '''Slices Controller GUI''' and some additional. These options, each shown in the figures '''A - H''' below, include:&lt;br /&gt;
&lt;br /&gt;
* A. Fit a slice to the size of a Viewer's window&lt;br /&gt;
* B. Adjust the opacity of a label map&lt;br /&gt;
* C. Show/Hide outlines around labels in a label map&lt;br /&gt;
* D. Show/Hide the Slice Reformat Widget&lt;br /&gt;
* E. Select options for compositing slice layers&lt;br /&gt;
* F. Choose manual or automatic slice spacing modes&lt;br /&gt;
* G. Create a lightbox view within a Slice Viewer&lt;br /&gt;
* H. Adjust the display of Foreground, Background or Label layers.&lt;br /&gt;
&lt;br /&gt;
[[image:SliceGUIMoreMap.png]]&lt;br /&gt;
&lt;br /&gt;
===Configuring Slice Viewers when the Controllers are collapsed ===&lt;br /&gt;
&lt;br /&gt;
In Slicer's '''Slices Module''', all Slice Viewers' Slice Controllers are arrayed in a vertical stack; When screen real estate must be maximized, the individual Slice Viewers' Controllers can be collapsed and the GUI panel's controllers can be used to manipulate the Viewers instead. The Slices Module's GUI panel is shown below.&lt;br /&gt;
&lt;br /&gt;
[[image:SlicesGUIPanel.png |center ]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Main 3D Viewer ==&lt;br /&gt;
&lt;br /&gt;
=== Default elements and their visibility===&lt;br /&gt;
&lt;br /&gt;
Slicer's Main 3D Viewer displays a three-dimensional view of the scene. By default, the scene includes some elements for spatial reference including a 3D wireframe cube centered around the origin (0,0,0) and labels along each of the principle axes ('''R'''ight, '''L'''eft, '''S'''uperior, '''I'''nferior, '''A'''nterior, and '''P'''osterior). Slicer's default blue background color, as well as the visibility of the spatial references in the view, can be modified in the View Control GUI panel's visibility menu, as shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-VCGuiVisibility.png]]&lt;br /&gt;
&lt;br /&gt;
=== Interacting ===&lt;br /&gt;
&lt;br /&gt;
You can adjust the view in the Main 3D Viewer using the mouse or keyboard (for information on the latter, please see the Keyboard Shortcuts section):&lt;br /&gt;
&lt;br /&gt;
* '''Zoom in:''' Right-mouse-button click-and-drag toward you. (Imagine pulling the scene closer)&lt;br /&gt;
* '''Zoom out:''' Right-mouse-button click-and-drag away from you. (Imagine pushing the scene away)&lt;br /&gt;
* '''Pan''' (shift the look-at point): Middle-mouse-button click-and-drag left, right, up or down.&lt;br /&gt;
* '''Rotate Around''' a look-at point: Left-mouse-button click-and-drag.&lt;br /&gt;
&lt;br /&gt;
If you need more precise control, or if the view gets into some hard-to-manage configuration, the View Control GUI panel can be used to reset the look-from and look-at point in a manageable way:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-VCGuiSetView.png]]&lt;br /&gt;
&lt;br /&gt;
=== Window and layout configurations ===&lt;br /&gt;
&lt;br /&gt;
Slicer can be configured to show or hide the Module GUI panel, and to display it on the left or right side of the Viewers. These options are accessed as follows:&lt;br /&gt;
&lt;br /&gt;
* Show/Hide Module GUI Panel: F5-key or Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]])-&amp;gt;Toggle GUI panel visibility&lt;br /&gt;
* Move Module GUI Panel to the Left/Right: Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]])-&amp;gt;Toggle GUI panel L/R&lt;br /&gt;
* Show/Hide Bottom Panel: F6-key (this option is only really useful in Slicer's Conventional View)&lt;br /&gt;
&lt;br /&gt;
[[image:AppGUIBasicConfigure.png]]&lt;br /&gt;
&lt;br /&gt;
In addition, there are a number of ways to arrange the Slice and 3D Viewers. We hope to offer a more extensible suite of configuration options in the future. At present, these options are available from Slicer's Application Toolbar's Layout Menubutton ([[image:AppDoc-layoutIcon.png]]), and are illustrated below:&lt;br /&gt;
&lt;br /&gt;
*&lt;br /&gt;
&lt;br /&gt;
[[image:AppLayouts.png]]&lt;br /&gt;
&lt;br /&gt;
= Error Log =&lt;br /&gt;
&lt;br /&gt;
Finally, the application has an accessible error log in the event of unexpected behavior or error messages -- this readout is useful for reporting bugs or usability problems back to the Slicer Development Team. The error log can be raised in the following ways:&lt;br /&gt;
&lt;br /&gt;
* Typing '''Ctrl+Alt+E'''&lt;br /&gt;
* Menubar's '''Window-&amp;gt;Error Log'''&lt;br /&gt;
* Clicking the '''Error Log icon''', which is displayed only if any error reports are present, and as shown below.&lt;br /&gt;
&lt;br /&gt;
[[image:RaiseErrorLog.png]]&lt;br /&gt;
&lt;br /&gt;
[[image:ErrorLog.png]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
= Status Text and Progress Bar =&lt;br /&gt;
&lt;br /&gt;
For some operations, loading, saving or processing may take awhile; Slicer may post status text at the bottom of the Application's window (shown below) that helps you to understand what it's working on. This readout isn't available as often as it should be; we hope to address this usability issue in future software releases. If you encounter any situation in which a status update would be especially useful but none exists, please report your discovery to Slicer's bug tracker as a usability issue.&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-StatusText.png  ]]&lt;br /&gt;
&lt;br /&gt;
Progress is also displayed during processing operations. One progress readout commonly used by command-line modules is found in the lower right corner of the Slicer Window in the Progress Gauge, shown below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ProgressBar.png |center ]]&lt;br /&gt;
&lt;br /&gt;
Some Slicer modules also use a pop-up progress dialog, which assumes &amp;quot;focus&amp;quot; and prevents you from interacting with Slicer until the processing is finished; the dialog appears as below:&lt;br /&gt;
&lt;br /&gt;
[[image:AppDoc-ProgressDialog.png |center ]]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Developers&amp;diff=9487</id>
		<title>Slicer3:Developers</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Developers&amp;diff=9487"/>
		<updated>2009-05-08T20:57:53Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Quick Links to Slicer3 Projects */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
= Slicer 3 Developer Page =&lt;br /&gt;
[[Image:3DSlicerLogo-H-Color-212x121.png|right]]&lt;br /&gt;
This page contains links to Slicer3 developer resources and events.&lt;br /&gt;
&lt;br /&gt;
Click here for &amp;lt;big&amp;gt;&amp;lt;big&amp;gt;'''[[Slicer3:Events|Slicer3 Events]]'''&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Slicer 3 Architecture Overview ==&lt;br /&gt;
For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).&lt;br /&gt;
&lt;br /&gt;
&amp;lt;gallery caption=&amp;quot;Highlights of the new architecture&amp;quot; widths=&amp;quot;200px&amp;quot;  perrow=&amp;quot;4&amp;quot;&amp;gt;&lt;br /&gt;
Image:Slicer3-Architecture.jpg&lt;br /&gt;
Image:Slicer3-Architecture-MRML.jpg&lt;br /&gt;
Image:Slicer3-Architecture-Layers.jpg&lt;br /&gt;
Image:ExecutionModelPlugins.png&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Quick Links for Developers ==&lt;br /&gt;
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers.  The content developed for the January 2007 AHM.&lt;br /&gt;
&lt;br /&gt;
{|align=&amp;quot;left&amp;quot; width=&amp;quot;1200px&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot; width=&amp;quot;60%&amp;quot;|'''Introduction to Slicer3'''&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Media:SlicerHistoricalTimeline.ppt | Slicer3 Historical Timeline]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Status_Summary | Status overview]] and [http://slicerl.bwh.harvard.edu/tmp/slicer3-PreAHMBeta%20Demo/slicer3-PreAHMBeta.htm Demo]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[Media:GUIMap.png|Schematic of application interface &amp;amp; functionality]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[Media:SliceGUI.png|Schematic of slice GUI]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Build_Instructions | Getting the software and troubleshooting]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot;|'''Two module types (Command line and Interactive)'''&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]]&lt;br /&gt;
||Jim and Bill [[media:Slicer3-ExecutionModelJune2006.ppt| Intro]]&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:How_to_implement_an_Interactive_Module_GUI | How to implement an interactive module]]&lt;br /&gt;
||Wendy&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot;|'''MRML'''&amp;lt;br/&amp;gt;Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms. [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides]&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]]&lt;br /&gt;
||Alex&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]]&lt;br /&gt;
||Alex&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Data_Model#Undo/Redo_Mechanism  | How undo/redo works, and how to enable it in your code]]&lt;br /&gt;
||Alex&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot;|'''GUI'''&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:StatelessGUI | Keeping the GUI stateless]]&lt;br /&gt;
||Wendy&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:EventBindings | Adding keyboard shortcuts]]&lt;br /&gt;
||Wendy&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines]]&lt;br /&gt;
||Wendy&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]]&lt;br /&gt;
||Wendy&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]]&lt;br /&gt;
||Wendy&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]]&lt;br /&gt;
||Jim&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]]&lt;br /&gt;
||Steve&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot;|'''Engineering'''&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&lt;br /&gt;
|-&lt;br /&gt;
||Tips for avoiding memory leaks:  Current Practice&lt;br /&gt;
||Steve&lt;br /&gt;
|-&lt;br /&gt;
||Tips for avoiding memory leaks:  [[Slicer3:Memory Management | Suggested change to SmartPointers]]&lt;br /&gt;
||Jim&lt;br /&gt;
|-&lt;br /&gt;
||Generating tests&lt;br /&gt;
||Bill&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Testing | Setting up Testing]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Builds | Build Information]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Launcher| The Launcher]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot;|'''Documenting your module'''&amp;lt;br/&amp;gt;As soon as the wiki page template is finalized, and the infrastructure is added to link to this wiki page from the &amp;quot;Help &amp;amp; Acknowledgment&amp;quot; panel in your module's GUI, we will ask developers to fill out a brief document describing your module and its use. Stay tuned for developments...&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:DocumentationWink|Documenting a module with wink]]&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot;|'''Integrate Slicer3 into a development environment'''&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3::Eclipse | Eclipse]]&lt;br /&gt;
||Michael Keilhack&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]&lt;br /&gt;
||&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Quick Links to Slicer3 Projects ==&lt;br /&gt;
Projects should correspond to the outstanding issues listed on the '''[[Slicer3:Status_Summary|Status Summary]]'''. Please refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.&lt;br /&gt;
&lt;br /&gt;
{|align=&amp;quot;left&amp;quot; width=&amp;quot;1200px&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot; width=&amp;quot;60%&amp;quot;|'''Slicer3 Projects'''&lt;br /&gt;
|bgcolor=&amp;quot;#ddf&amp;quot; valign=&amp;quot;top&amp;quot;|'''Key People'''&amp;lt;br/&amp;gt;Bold names are responsible for an aspect of the project.&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Architecture/Features|Architecture/Features]]&lt;br /&gt;
||'''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Data_Model|Data Model / libMRML]]&lt;br /&gt;
||'''Alex''', Steve&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]&lt;br /&gt;
||'''Jim Miller''', Bill Lorensen&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Interface_Design|Interface Design and Usability ]]&lt;br /&gt;
||'''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]&lt;br /&gt;
||'''Nicole''', Katie, Wendy, Mathieu&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:DTMRI|DTMRI]]&lt;br /&gt;
||'''Alex''' with help from Diffusion Images:  '''Raul''', Tractography: '''Lauren''' [http://lmi.bwh.harvard.edu LMI]&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Editor|Editor]]&lt;br /&gt;
||'''Steve'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]&lt;br /&gt;
||'''Nicole'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]&lt;br /&gt;
||'''Haiying'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:EM|EMSegment Interface]]&lt;br /&gt;
||'''Brad Davis'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]&lt;br /&gt;
||'''Steve Pieper'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]&lt;br /&gt;
||'''Andy''', Katie&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]&lt;br /&gt;
||'''Jags'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]&lt;br /&gt;
||'''Julien Jomier'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Registration|Registration Modules]]&lt;br /&gt;
||'''Jim Miller''', Steve Pieper&lt;br /&gt;
|-&lt;br /&gt;
||[http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization Improvements to the registration framework]&lt;br /&gt;
||'''Stephen Aylward'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Python|Python Integration]]&lt;br /&gt;
||'''Dan Blezek'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Grid_Interface|Grid Integration]]&lt;br /&gt;
||'''Jeff Grethe''', Neil&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]&lt;br /&gt;
||'''Katie'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:ThreadingToolKit|Threading ToolKit]]&lt;br /&gt;
||'''Dan Blezek, James Miller, Stephen Aylward'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Volume Rendering |Volume Rendering]]&lt;br /&gt;
||'''Andy'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA]]&lt;br /&gt;
||'''Ben'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:XNAT |XNAT Interface]]&lt;br /&gt;
||'''Steve''', Wendy, Dan Marcus, Tim Olsen&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:LDDMM |LDDMM Interface]]&lt;br /&gt;
||'''Steve''', Anthony Kolasny&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Web Presence |Web Presence]]&lt;br /&gt;
||'''Nicole Aucoin''', Zack Galbreath&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Loadable Modules |Loadable Modules]]&lt;br /&gt;
||'''Alex Yarmarkovich''', Steve Pieper&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Extensions |Extensions]]&lt;br /&gt;
||Steve Peiper&lt;br /&gt;
|-&lt;br /&gt;
||[http://www.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation Diffusion Editor]&lt;br /&gt;
||'''Kerstin'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]&lt;br /&gt;
||Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Remote Data Handling | Remote Data Handling]]&lt;br /&gt;
||Steve Pieper, Nicole Aucoin, Wendy Plesniak&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Module:QueryAtlas |Query Atlas]]&lt;br /&gt;
||'''Wendy Plesniak'''&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:MistSlicer | MistSlicer]]&lt;br /&gt;
||'''Yuichiro Hayashi''', Kensaku Mori, Nobuhiko Hata&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:RadiologicalReview | Radiological review]]&lt;br /&gt;
||'''Jim Miller'''&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Slicer 3 Quick links to the Source code ==&lt;br /&gt;
The Slicer3 svn repository:&lt;br /&gt;
&lt;br /&gt;
 svn co http://svn.slicer.org/Slicer3/trunk Slicer3&lt;br /&gt;
&lt;br /&gt;
{|align=&amp;quot;left&amp;quot; width=&amp;quot;1200px&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot; width=&amp;quot;60%&amp;quot;|'''General Slicer3 Quick Links'''&lt;br /&gt;
|style=&amp;quot;background:#ddf&amp;quot; width=&amp;quot;40%&amp;quot;|'''Debugging Slicer3 Quick Links'''&lt;br /&gt;
|-&lt;br /&gt;
||[http://www.na-mic.org/Wiki/index.php/Engineering:SandBox Instructions for NA-MIC svn]&lt;br /&gt;
||[http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 Dashboard (As Of May 2, 2008)]&lt;br /&gt;
|-&lt;br /&gt;
||Use [http://viewvc.slicer.org ViewVC to browse the repository]&lt;br /&gt;
||[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard (Before May 2, 2008)]&lt;br /&gt;
|-&lt;br /&gt;
||[[Slicer3:Build_Instructions|Slicer3 build instructions]]&lt;br /&gt;
||[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]&lt;br /&gt;
|-&lt;br /&gt;
||[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Doxygen documentation for Slicer3].&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.&lt;br /&gt;
||&lt;br /&gt;
|-&lt;br /&gt;
||Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== ====&lt;br /&gt;
Discussion of Slicer3 takes place on the slicer-devel at massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: slicer-devel-request at massmail.spl.harvard.edu  with the keyword '''''subscribe''''' as the subject.  Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].&lt;br /&gt;
&lt;br /&gt;
== Design Information ==&lt;br /&gt;
*May 23, 2006: [http://www.na-mic.org/Wiki/index.php/Algorithms:Core1Visit_May06 Algorithm Core workshop.]&lt;br /&gt;
*April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9486</id>
		<title>Slicer3:Extensions</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Extensions&amp;diff=9486"/>
		<updated>2009-05-08T20:49:12Z</updated>

		<summary type="html">&lt;p&gt;Tgl: New page: 3D Slicer now supports extensions.  Extensions are available from an extension server.  This allows end-users to select the extensions useful to them, without having to download the entire...&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;3D Slicer now supports extensions.  Extensions are available from an extension server.  This allows end-users to select the extensions useful to them, without having to download the entire extension archive.&lt;br /&gt;
&lt;br /&gt;
== FOR DEVELOPERS ==&lt;br /&gt;
&lt;br /&gt;
To enable your Command Line, Scripted, Loadable, or Loadable GUI-less module, add an &amp;quot;s3ext&amp;quot; script to the /Slicer3/Extensions directory of the source repository:&lt;br /&gt;
&lt;br /&gt;
ExampleLoadableModule.s3ext:&lt;br /&gt;
  scm       svn&lt;br /&gt;
  svnpath   https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules/Loadable&lt;br /&gt;
  svnusername slicerbot&lt;br /&gt;
  svnpassword slicer&lt;br /&gt;
  &lt;br /&gt;
  depends&lt;br /&gt;
  &lt;br /&gt;
  homepage  http://www.nitrc.org/projects/slicer3examples/&lt;br /&gt;
  &lt;br /&gt;
  category  Examples&lt;br /&gt;
  &lt;br /&gt;
  status    Beta&lt;br /&gt;
  &lt;br /&gt;
  description An example of a loadable module using Slicer3 GUI and Logic classes, plus a MRML node.&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=9485</id>
		<title>Slicer3:Loadable Modules:HOWTO</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=9485"/>
		<updated>2009-05-08T20:44:46Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Slicer3 Extension Description */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;In order to allow a module to be detected and loaded at runtime a number of changes are required.  The first is within the module's GUI class.  The vtkSlicerModuleGUI-derived class _must_ implement &amp;quot;void SetModuleLogic(vtkSlicerLogic*)&amp;quot;.  This allows the library loading methods to load the GUI without knowing the specific class type.&lt;br /&gt;
&lt;br /&gt;
A text file named after the module must also be created.&lt;br /&gt;
&lt;br /&gt;
Last, macros for module creation and handling must be added to the CMakeLists file.&lt;br /&gt;
&lt;br /&gt;
For more information on these edits, plus some optional changes, see below.&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameGUI ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameGUI.h/cxx&lt;br /&gt;
&lt;br /&gt;
'''Do not create this class if you want your module to be GUI-less'''&lt;br /&gt;
&lt;br /&gt;
=== Required ===&lt;br /&gt;
&lt;br /&gt;
For your vtkSlicerModuleGUI-derived class, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual void SetModuleLogic(vtkSlicerLogic*)&lt;br /&gt;
&lt;br /&gt;
This is necessary so that the Loadable module code does not need to cast the Logic pointer returned from the defined entry point.&lt;br /&gt;
&lt;br /&gt;
=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
&lt;br /&gt;
To add module-specific initialization code, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual void Init();&lt;br /&gt;
&lt;br /&gt;
This is useful to have your module register callbacks for Picking (See QdecModule).&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameLogic ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameLogic.h/cxx&lt;br /&gt;
&lt;br /&gt;
=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
&lt;br /&gt;
== ModuleName.xml ==&lt;br /&gt;
&lt;br /&gt;
ModuleName.xml&lt;br /&gt;
&lt;br /&gt;
Create ModuleName.xml in the module's directory.  ModuleName should follow the naming convention for the *GUI and *Logic classes.&lt;br /&gt;
&lt;br /&gt;
For example, with two classes named vtkOpenIGTLinkLogic &amp;amp; vtkOpenIGTLinkGUI, create an XML file named OpenIGTLink.xml&lt;br /&gt;
&lt;br /&gt;
This file contains naming directives, as well as lists dependencies.  At a minimum, the module name &amp;amp; GUI name must be specified:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Name&amp;gt;Open IGT Link&amp;lt;/Name&amp;gt;&lt;br /&gt;
  &amp;lt;GUIName&amp;gt;OpenIGT&amp;lt;/GUIName&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''When creating a GUI-less module, omit the GUIName directive.'''&lt;br /&gt;
&lt;br /&gt;
Optionally, other attributes may be listed:&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Description&amp;gt;This is a description of my module.&amp;lt;/Description&amp;gt;&lt;br /&gt;
  &amp;lt;SourceLocation&amp;gt;https://use/the/source/luke&amp;lt;/SourceLocation&amp;gt;&lt;br /&gt;
  &amp;lt;HomePage&amp;gt;http://my/module/homepage&amp;lt;/HomePage&amp;gt;&lt;br /&gt;
  &amp;lt;Version&amp;gt;1.0&amp;lt;/Version&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module One&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module Two&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Author&amp;gt;Karl Fardman&amp;lt;/Author&amp;gt;&lt;br /&gt;
  &amp;lt;Acknowledgement&amp;gt;All the little people&amp;lt;/Acknowledgement&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== CMakeLists.txt ==&lt;br /&gt;
&lt;br /&gt;
CMakeLists.txt&lt;br /&gt;
&lt;br /&gt;
Most modules will be defined outside of the main Slicer3 build tree.  To enable your module to be loaded dynamically, a couple entries in CMakeLists.txt are required.&lt;br /&gt;
&lt;br /&gt;
Near the top of the file, include the directives that will locate the Slicer 3 build tree:&lt;br /&gt;
&lt;br /&gt;
  if(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
    find_package(Slicer3 REQUIRED)&lt;br /&gt;
    include(${Slicer3_USE_FILE})&lt;br /&gt;
    slicer3_set_default_install_prefix_for_external_projects()&lt;br /&gt;
  endif(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
&lt;br /&gt;
Next, tell CMake to generate the supporting files for Loadable Module:&lt;br /&gt;
&lt;br /&gt;
  generatelm(OpenIGTLink_SRCS OpenIGTLink.txt)&lt;br /&gt;
&lt;br /&gt;
NOTE:  The macro should be placed after TCL wrapping is done, as it adds to the source variable. For more details, check the [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/NeuroNav/CMakeLists.txt NeuroNav module CMakeLists.txt] file, as it provides a good starting point.&lt;br /&gt;
 &lt;br /&gt;
Finally, direct CMake to copy the binary files to the Slicer3 library location.  This should be the last entry in your CMakeLists file:&lt;br /&gt;
&lt;br /&gt;
  install(TARGETS ${lib_name}&lt;br /&gt;
    RUNTIME DESTINATION ${Slicer3_INSTALL_MODULES_BIN_DIR} COMPONENT RuntimeLibraries &lt;br /&gt;
    LIBRARY DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT RuntimeLibraries&lt;br /&gt;
    ARCHIVE DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT Development&lt;br /&gt;
    )&lt;br /&gt;
&lt;br /&gt;
== Slicer3 Extension Description ==&lt;br /&gt;
&lt;br /&gt;
In order to add the module to the extension server, a Slicer3 Extension file needs to be added to /Slicer3/Extensions:&lt;br /&gt;
&lt;br /&gt;
  scm       svn&lt;br /&gt;
  svnpath   https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules/Loadable&lt;br /&gt;
  svnusername slicerbot&lt;br /&gt;
  svnpassword slicer&lt;br /&gt;
  &lt;br /&gt;
  depends&lt;br /&gt;
  &lt;br /&gt;
  homepage  http://www.nitrc.org/projects/slicer3examples/&lt;br /&gt;
  &lt;br /&gt;
  category  Examples&lt;br /&gt;
  &lt;br /&gt;
  status    Beta&lt;br /&gt;
  &lt;br /&gt;
  description An example of a loadable module using Slicer3 GUI and Logic classes, plus a MRML node.&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/53jqbp Loadable Module]&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/c6e7ab Loadable GUI-less Module]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=9484</id>
		<title>Slicer3:Loadable Modules:HOWTO</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=9484"/>
		<updated>2009-05-08T20:38:41Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Slicer3 Extension Description */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;In order to allow a module to be detected and loaded at runtime a number of changes are required.  The first is within the module's GUI class.  The vtkSlicerModuleGUI-derived class _must_ implement &amp;quot;void SetModuleLogic(vtkSlicerLogic*)&amp;quot;.  This allows the library loading methods to load the GUI without knowing the specific class type.&lt;br /&gt;
&lt;br /&gt;
A text file named after the module must also be created.&lt;br /&gt;
&lt;br /&gt;
Last, macros for module creation and handling must be added to the CMakeLists file.&lt;br /&gt;
&lt;br /&gt;
For more information on these edits, plus some optional changes, see below.&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameGUI ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameGUI.h/cxx&lt;br /&gt;
&lt;br /&gt;
'''Do not create this class if you want your module to be GUI-less'''&lt;br /&gt;
&lt;br /&gt;
=== Required ===&lt;br /&gt;
&lt;br /&gt;
For your vtkSlicerModuleGUI-derived class, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual void SetModuleLogic(vtkSlicerLogic*)&lt;br /&gt;
&lt;br /&gt;
This is necessary so that the Loadable module code does not need to cast the Logic pointer returned from the defined entry point.&lt;br /&gt;
&lt;br /&gt;
=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
&lt;br /&gt;
To add module-specific initialization code, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual void Init();&lt;br /&gt;
&lt;br /&gt;
This is useful to have your module register callbacks for Picking (See QdecModule).&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameLogic ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameLogic.h/cxx&lt;br /&gt;
&lt;br /&gt;
=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
&lt;br /&gt;
== ModuleName.xml ==&lt;br /&gt;
&lt;br /&gt;
ModuleName.xml&lt;br /&gt;
&lt;br /&gt;
Create ModuleName.xml in the module's directory.  ModuleName should follow the naming convention for the *GUI and *Logic classes.&lt;br /&gt;
&lt;br /&gt;
For example, with two classes named vtkOpenIGTLinkLogic &amp;amp; vtkOpenIGTLinkGUI, create an XML file named OpenIGTLink.xml&lt;br /&gt;
&lt;br /&gt;
This file contains naming directives, as well as lists dependencies.  At a minimum, the module name &amp;amp; GUI name must be specified:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Name&amp;gt;Open IGT Link&amp;lt;/Name&amp;gt;&lt;br /&gt;
  &amp;lt;GUIName&amp;gt;OpenIGT&amp;lt;/GUIName&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''When creating a GUI-less module, omit the GUIName directive.'''&lt;br /&gt;
&lt;br /&gt;
Optionally, other attributes may be listed:&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Description&amp;gt;This is a description of my module.&amp;lt;/Description&amp;gt;&lt;br /&gt;
  &amp;lt;SourceLocation&amp;gt;https://use/the/source/luke&amp;lt;/SourceLocation&amp;gt;&lt;br /&gt;
  &amp;lt;HomePage&amp;gt;http://my/module/homepage&amp;lt;/HomePage&amp;gt;&lt;br /&gt;
  &amp;lt;Version&amp;gt;1.0&amp;lt;/Version&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module One&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module Two&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Author&amp;gt;Karl Fardman&amp;lt;/Author&amp;gt;&lt;br /&gt;
  &amp;lt;Acknowledgement&amp;gt;All the little people&amp;lt;/Acknowledgement&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== CMakeLists.txt ==&lt;br /&gt;
&lt;br /&gt;
CMakeLists.txt&lt;br /&gt;
&lt;br /&gt;
Most modules will be defined outside of the main Slicer3 build tree.  To enable your module to be loaded dynamically, a couple entries in CMakeLists.txt are required.&lt;br /&gt;
&lt;br /&gt;
Near the top of the file, include the directives that will locate the Slicer 3 build tree:&lt;br /&gt;
&lt;br /&gt;
  if(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
    find_package(Slicer3 REQUIRED)&lt;br /&gt;
    include(${Slicer3_USE_FILE})&lt;br /&gt;
    slicer3_set_default_install_prefix_for_external_projects()&lt;br /&gt;
  endif(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
&lt;br /&gt;
Next, tell CMake to generate the supporting files for Loadable Module:&lt;br /&gt;
&lt;br /&gt;
  generatelm(OpenIGTLink_SRCS OpenIGTLink.txt)&lt;br /&gt;
&lt;br /&gt;
NOTE:  The macro should be placed after TCL wrapping is done, as it adds to the source variable. For more details, check the [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/NeuroNav/CMakeLists.txt NeuroNav module CMakeLists.txt] file, as it provides a good starting point.&lt;br /&gt;
 &lt;br /&gt;
Finally, direct CMake to copy the binary files to the Slicer3 library location.  This should be the last entry in your CMakeLists file:&lt;br /&gt;
&lt;br /&gt;
  install(TARGETS ${lib_name}&lt;br /&gt;
    RUNTIME DESTINATION ${Slicer3_INSTALL_MODULES_BIN_DIR} COMPONENT RuntimeLibraries &lt;br /&gt;
    LIBRARY DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT RuntimeLibraries&lt;br /&gt;
    ARCHIVE DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT Development&lt;br /&gt;
    )&lt;br /&gt;
&lt;br /&gt;
== Slicer3 Extension Description ==&lt;br /&gt;
&lt;br /&gt;
In order to add the module to the extension server, and Slicer3 Extension file needs to be added to /Slicer3/Extensions:&lt;br /&gt;
&lt;br /&gt;
  scm       svn&lt;br /&gt;
  svnpath   https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules/Loadable&lt;br /&gt;
  svnusername slicerbot&lt;br /&gt;
  svnpassword slicer&lt;br /&gt;
  &lt;br /&gt;
  depends&lt;br /&gt;
  &lt;br /&gt;
  homepage  http://www.nitrc.org/projects/slicer3examples/&lt;br /&gt;
  &lt;br /&gt;
  category  Examples&lt;br /&gt;
  &lt;br /&gt;
  status    Beta&lt;br /&gt;
  &lt;br /&gt;
  description An example of a loadable module using Slicer3 GUI and Logic classes, plus a MRML node.&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/53jqbp Loadable Module]&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/c6e7ab Loadable GUI-less Module]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=9483</id>
		<title>Slicer3:Loadable Modules:HOWTO</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=9483"/>
		<updated>2009-05-08T20:38:25Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;In order to allow a module to be detected and loaded at runtime a number of changes are required.  The first is within the module's GUI class.  The vtkSlicerModuleGUI-derived class _must_ implement &amp;quot;void SetModuleLogic(vtkSlicerLogic*)&amp;quot;.  This allows the library loading methods to load the GUI without knowing the specific class type.&lt;br /&gt;
&lt;br /&gt;
A text file named after the module must also be created.&lt;br /&gt;
&lt;br /&gt;
Last, macros for module creation and handling must be added to the CMakeLists file.&lt;br /&gt;
&lt;br /&gt;
For more information on these edits, plus some optional changes, see below.&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameGUI ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameGUI.h/cxx&lt;br /&gt;
&lt;br /&gt;
'''Do not create this class if you want your module to be GUI-less'''&lt;br /&gt;
&lt;br /&gt;
=== Required ===&lt;br /&gt;
&lt;br /&gt;
For your vtkSlicerModuleGUI-derived class, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual void SetModuleLogic(vtkSlicerLogic*)&lt;br /&gt;
&lt;br /&gt;
This is necessary so that the Loadable module code does not need to cast the Logic pointer returned from the defined entry point.&lt;br /&gt;
&lt;br /&gt;
=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
&lt;br /&gt;
To add module-specific initialization code, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual void Init();&lt;br /&gt;
&lt;br /&gt;
This is useful to have your module register callbacks for Picking (See QdecModule).&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameLogic ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameLogic.h/cxx&lt;br /&gt;
&lt;br /&gt;
=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
&lt;br /&gt;
== ModuleName.xml ==&lt;br /&gt;
&lt;br /&gt;
ModuleName.xml&lt;br /&gt;
&lt;br /&gt;
Create ModuleName.xml in the module's directory.  ModuleName should follow the naming convention for the *GUI and *Logic classes.&lt;br /&gt;
&lt;br /&gt;
For example, with two classes named vtkOpenIGTLinkLogic &amp;amp; vtkOpenIGTLinkGUI, create an XML file named OpenIGTLink.xml&lt;br /&gt;
&lt;br /&gt;
This file contains naming directives, as well as lists dependencies.  At a minimum, the module name &amp;amp; GUI name must be specified:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Name&amp;gt;Open IGT Link&amp;lt;/Name&amp;gt;&lt;br /&gt;
  &amp;lt;GUIName&amp;gt;OpenIGT&amp;lt;/GUIName&amp;gt;&lt;br /&gt;
&lt;br /&gt;
'''When creating a GUI-less module, omit the GUIName directive.'''&lt;br /&gt;
&lt;br /&gt;
Optionally, other attributes may be listed:&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Description&amp;gt;This is a description of my module.&amp;lt;/Description&amp;gt;&lt;br /&gt;
  &amp;lt;SourceLocation&amp;gt;https://use/the/source/luke&amp;lt;/SourceLocation&amp;gt;&lt;br /&gt;
  &amp;lt;HomePage&amp;gt;http://my/module/homepage&amp;lt;/HomePage&amp;gt;&lt;br /&gt;
  &amp;lt;Version&amp;gt;1.0&amp;lt;/Version&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module One&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module Two&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Author&amp;gt;Karl Fardman&amp;lt;/Author&amp;gt;&lt;br /&gt;
  &amp;lt;Acknowledgement&amp;gt;All the little people&amp;lt;/Acknowledgement&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== CMakeLists.txt ==&lt;br /&gt;
&lt;br /&gt;
CMakeLists.txt&lt;br /&gt;
&lt;br /&gt;
Most modules will be defined outside of the main Slicer3 build tree.  To enable your module to be loaded dynamically, a couple entries in CMakeLists.txt are required.&lt;br /&gt;
&lt;br /&gt;
Near the top of the file, include the directives that will locate the Slicer 3 build tree:&lt;br /&gt;
&lt;br /&gt;
  if(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
    find_package(Slicer3 REQUIRED)&lt;br /&gt;
    include(${Slicer3_USE_FILE})&lt;br /&gt;
    slicer3_set_default_install_prefix_for_external_projects()&lt;br /&gt;
  endif(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
&lt;br /&gt;
Next, tell CMake to generate the supporting files for Loadable Module:&lt;br /&gt;
&lt;br /&gt;
  generatelm(OpenIGTLink_SRCS OpenIGTLink.txt)&lt;br /&gt;
&lt;br /&gt;
NOTE:  The macro should be placed after TCL wrapping is done, as it adds to the source variable. For more details, check the [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/NeuroNav/CMakeLists.txt NeuroNav module CMakeLists.txt] file, as it provides a good starting point.&lt;br /&gt;
 &lt;br /&gt;
Finally, direct CMake to copy the binary files to the Slicer3 library location.  This should be the last entry in your CMakeLists file:&lt;br /&gt;
&lt;br /&gt;
  install(TARGETS ${lib_name}&lt;br /&gt;
    RUNTIME DESTINATION ${Slicer3_INSTALL_MODULES_BIN_DIR} COMPONENT RuntimeLibraries &lt;br /&gt;
    LIBRARY DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT RuntimeLibraries&lt;br /&gt;
    ARCHIVE DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT Development&lt;br /&gt;
    )&lt;br /&gt;
&lt;br /&gt;
== Slicer3 Extension Description ==&lt;br /&gt;
&lt;br /&gt;
In order to add the module to the extension server, and Slicer3 Extension file needs to be added to /Slicer3/Extensions:&lt;br /&gt;
&lt;br /&gt;
  scm       svn&lt;br /&gt;
  svnpath   https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules/Loadable&lt;br /&gt;
  svnusername slicerbot&lt;br /&gt;
  svnpassword slicer&lt;br /&gt;
&lt;br /&gt;
  depends&lt;br /&gt;
&lt;br /&gt;
  homepage  http://www.nitrc.org/projects/slicer3examples/&lt;br /&gt;
&lt;br /&gt;
  category  Examples&lt;br /&gt;
&lt;br /&gt;
  status    Beta&lt;br /&gt;
&lt;br /&gt;
  description An example of a loadable module using Slicer3 GUI and Logic classes, plus a MRML node.&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/53jqbp Loadable Module]&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/c6e7ab Loadable GUI-less Module]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules&amp;diff=9482</id>
		<title>Slicer3:Loadable Modules</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules&amp;diff=9482"/>
		<updated>2009-05-08T20:36:17Z</updated>

		<summary type="html">&lt;p&gt;Tgl: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Introduction ==&lt;br /&gt;
&lt;br /&gt;
This feature allows Slicer3 modules to be detected and loaded at run-time.  This enables module binaries to be added to Slicer3 without having to be compiled and linked with the main binary.&lt;br /&gt;
&lt;br /&gt;
Module authors should create their modules based on templates like the [http://na-mic.org/ViewVC/index.cgi/trunk/Modules/GradientAnisotropicDiffusionFilter/?sortby=file#dirlist GAD Module] found in the Slicer3 Modules/ subdirectory.  There will be a future version of Slicer3 that allows users to download and use modules from an online module archive.&lt;br /&gt;
&lt;br /&gt;
Loadable modules in Slicer3: [[Slicer3:Loadable_Modules:Current]]&lt;br /&gt;
&lt;br /&gt;
== For Developers ==&lt;br /&gt;
&lt;br /&gt;
For information on how to make your module loadable: [[Slicer3:Loadable_Modules:HOWTO]]&lt;br /&gt;
&lt;br /&gt;
[[Slicer3:Loadable_Modules:Working_Plans]]&lt;br /&gt;
&lt;br /&gt;
[[Slicer3:Loadable_Modules:Status_2009-01-20]]&lt;br /&gt;
&lt;br /&gt;
See materials from [http://www.na-mic.org/Wiki/index.php/AHM2009:NITRC_and_Slicer dissusion at 2009 NA-MIC All Hands Meeting].&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
	</entry>
	<entry>
		<id>https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=8235</id>
		<title>Slicer3:Loadable Modules:HOWTO</title>
		<link rel="alternate" type="text/html" href="https://www.slicer.org/w/index.php?title=Slicer3:Loadable_Modules:HOWTO&amp;diff=8235"/>
		<updated>2009-02-28T22:22:30Z</updated>

		<summary type="html">&lt;p&gt;Tgl: /* Example */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;In order to allow a module to be detected and loaded at runtime a number of changes are required.  The first is within the module's GUI class.  The vtkSlicerModuleGUI-derived class _must_ implement &amp;quot;void SetModuleLogic(vtkSlicerLogic*)&amp;quot;.  This allows the library loading methods to load the GUI without knowing the specific class type.&lt;br /&gt;
&lt;br /&gt;
A text file named after the module must also be created.&lt;br /&gt;
&lt;br /&gt;
Last, macros for module creation and handling must be added to the CMakeLists file.&lt;br /&gt;
&lt;br /&gt;
For more information on these edits, plus some optional changes, see below.&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameGUI ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameGUI.h/cxx&lt;br /&gt;
&lt;br /&gt;
'''Do not create this class if you want your module to be GUI-less'''&lt;br /&gt;
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=== Required ===&lt;br /&gt;
&lt;br /&gt;
For your vtkSlicerModuleGUI-derived class, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual void SetModuleLogic(vtkSlicerLogic*)&lt;br /&gt;
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This is necessary so that the Loadable module code does not need to cast the Logic pointer returned from the defined entry point.&lt;br /&gt;
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=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
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  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
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To add module-specific initialization code, declare and implement:&lt;br /&gt;
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  virtual void Init();&lt;br /&gt;
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This is useful to have your module register callbacks for Picking (See QdecModule).&lt;br /&gt;
&lt;br /&gt;
== vtkModuleNameLogic ==&lt;br /&gt;
&lt;br /&gt;
vtkModuleNameLogic.h/cxx&lt;br /&gt;
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=== Optional ===&lt;br /&gt;
&lt;br /&gt;
To add module-specific MRML events to observe, declare and implement:&lt;br /&gt;
&lt;br /&gt;
  virtual vtkIntArray* NewObservableEvents();&lt;br /&gt;
&lt;br /&gt;
== ModuleName.xml ==&lt;br /&gt;
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ModuleName.xml&lt;br /&gt;
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Create ModuleName.xml in the module's directory.  ModuleName should follow the naming convention for the *GUI and *Logic classes.&lt;br /&gt;
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For example, with two classes named vtkOpenIGTLinkLogic &amp;amp; vtkOpenIGTLinkGUI, create an XML file named OpenIGTLink.xml&lt;br /&gt;
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This file contains naming directives, as well as lists dependencies.  At a minimum, the module name &amp;amp; GUI name must be specified:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Name&amp;gt;Open IGT Link&amp;lt;/Name&amp;gt;&lt;br /&gt;
  &amp;lt;GUIName&amp;gt;OpenIGT&amp;lt;/GUIName&amp;gt;&lt;br /&gt;
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'''When creating a GUI-less module, omit the GUIName directive.'''&lt;br /&gt;
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Optionally, other attributes may be listed:&lt;br /&gt;
&lt;br /&gt;
  &amp;lt;Description&amp;gt;This is a description of my module.&amp;lt;/Description&amp;gt;&lt;br /&gt;
  &amp;lt;SourceLocation&amp;gt;https://use/the/source/luke&amp;lt;/SourceLocation&amp;gt;&lt;br /&gt;
  &amp;lt;HomePage&amp;gt;http://my/module/homepage&amp;lt;/HomePage&amp;gt;&lt;br /&gt;
  &amp;lt;Version&amp;gt;1.0&amp;lt;/Version&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module One&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Dependency&amp;gt;Module Two&amp;lt;/Dependency&amp;gt;&lt;br /&gt;
  &amp;lt;Author&amp;gt;Karl Fardman&amp;lt;/Author&amp;gt;&lt;br /&gt;
  &amp;lt;Acknowledgement&amp;gt;All the little people&amp;lt;/Acknowledgement&amp;gt;&lt;br /&gt;
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== CMakeLists.txt ==&lt;br /&gt;
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CMakeLists.txt&lt;br /&gt;
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Most modules will be defined outside of the main Slicer3 build tree.  To enable your module to be loaded dynamically, a couple entries in CMakeLists.txt are required.&lt;br /&gt;
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Near the top of the file, include the directives that will locate the Slicer 3 build tree:&lt;br /&gt;
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  if(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
    find_package(Slicer3 REQUIRED)&lt;br /&gt;
    include(${Slicer3_USE_FILE})&lt;br /&gt;
    slicer3_set_default_install_prefix_for_external_projects()&lt;br /&gt;
  endif(NOT Slicer3_SOURCE_DIR)&lt;br /&gt;
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Next, tell CMake to generate the supporting files for Loadable Module:&lt;br /&gt;
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  generatelm(OpenIGTLink_SRCS OpenIGTLink.txt)&lt;br /&gt;
&lt;br /&gt;
NOTE:  The macro should be placed after TCL wrapping is done, as it adds to the source variable. For more details, check the [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/NeuroNav/CMakeLists.txt NeuroNav module CMakeLists.txt] file, as it provides a good starting point.&lt;br /&gt;
 &lt;br /&gt;
Finally, direct CMake to copy the binary files to the Slicer3 library location.  This should be the last entry in your CMakeLists file:&lt;br /&gt;
&lt;br /&gt;
  install(TARGETS ${lib_name}&lt;br /&gt;
    RUNTIME DESTINATION ${Slicer3_INSTALL_MODULES_BIN_DIR} COMPONENT RuntimeLibraries &lt;br /&gt;
    LIBRARY DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT RuntimeLibraries&lt;br /&gt;
    ARCHIVE DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR} COMPONENT Development&lt;br /&gt;
    )&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/53jqbp Loadable Module]&lt;br /&gt;
&lt;br /&gt;
[http://tinyurl.com/c6e7ab Loadable GUI-less Module]&lt;/div&gt;</summary>
		<author><name>Tgl</name></author>
		
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