Slicer Wiki - User contributions [en]

Template:Documentation/4.10/slicerapplication-header

2018-10-19T00:48:36Z

UpdateBot: Nightly -> 4.10

<includeonly>{{documentation/{{documentation/version}}/header}}</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/slicerapplication-header}}</pre>

{{documentation/{{documentation/version}}/slicerapplication-header}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/qtversion

2018-10-19T00:48:35Z

UpdateBot: Nightly -> 4.10

<includeonly>4.7.4</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/qtversion}}</pre>

{{documentation/{{documentation/version}}/qtversion}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/slicerapplication-footer

2018-10-19T00:48:35Z

UpdateBot: Nightly -> 4.10

<includeonly>[[Category:Documentation/{{documentation/version}}/SlicerApplication|{{#titleparts: {{PAGENAME}} | 1 | 4 }}]]</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/slicerapplication-footer}}</pre>



[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-subsubsection

2018-10-19T00:48:34Z

UpdateBot: Nightly -> 4.10

<includeonly>=== {{{1}}} ===</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-subsubsection|Awesome stuff}}</pre>

{{documentation/{{documentation/version}}/module-subsubsection|Awesome stuff}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-subsubsubsection

2018-10-19T00:48:34Z

UpdateBot: Nightly -> 4.10

<includeonly>==== {{{1}}} ====</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-subsubsubsection|Awesome stuff}}</pre>

{{documentation/{{documentation/version}}/module-subsubsubsection|Awesome stuff}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-type

2018-10-19T00:48:34Z

UpdateBot: Nightly -> 4.10

<includeonly>Type: {{{1}}}</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-type|Interactive}}</pre>

{{documentation/{{documentation/version}}/module-type|Interactive}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-qtscriptedloadable-xmlurl

2018-10-19T00:48:33Z

UpdateBot: Nightly -> 4.10

<includeonly>http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/{{{1}}}.xml?revision={{{2}}}&view=co</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-qtscriptedloadable-xmlurl|Endoscopy|18393}}</pre>

{{documentation/{{documentation/version}}/module-qtscriptedloadable-xmlurl|Endoscopy|18393}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-section

2018-10-19T00:48:33Z

UpdateBot: Nightly -> 4.10

<includeonly>= {{{1}}} =</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-section|Awesome stuff}}</pre>

{{documentation/{{documentation/version}}/module-section|Awesome stuff}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-subsection

2018-10-19T00:48:33Z

UpdateBot: Nightly -> 4.10

<includeonly>== {{{1}}} ==</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-subsection|Awesome stuff}}</pre>

{{documentation/{{documentation/version}}/module-subsection|Awesome stuff}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-parametersdescription

2018-10-19T00:48:32Z

UpdateBot: Nightly -> 4.10

<includeonly>Parameters:
{{#get_web_data:
url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/ModulesMetadata}}
|format=CSV with header
|data=xmldescriptionurl=XMLDescriptionURL
|filters=Name={{documentation/modulename}}
}}{{#xsl: https://gist.githubusercontent.com/jcfr/1303059/raw/2300b4dc3991c2af6903e0a2fff7f119146575af/slicer-4.0-module-parameterdescription.xsl | {{#external_value:xmldescriptionurl}} | parse=true | nocache = false}}
{{#get_web_data:
url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/ModulesMetadata}}
|format=CSV with header
|data=xmldescriptionurl=XMLDescriptionURL
|filters=Name={{documentation/modulename}}
}}
List of parameters generated transforming [{{#external_value:xmldescriptionurl}} this XML file] using [https://gist.githubusercontent.com/jcfr/1303059/raw/2300b4dc3991c2af6903e0a2fff7f119146575af/slicer-4.0-module-parameterdescription.xsl this XSL file]. To update the URL of the XML file, edit [[Documentation/{{documentation/version}}/ModulesMetadata|this page]]. 
</includeonly><noinclude>

== Usage ==

{{pre2|scroll|<nowiki>{{documentation/{{documentation/version}}/module-parametersdescription}} </nowiki>}}

{{note}}Since this template is not specific to a given module. Exercising the template would return an empty string.

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-qtloadable-xmlurl

2018-10-19T00:48:32Z

UpdateBot: Nightly -> 4.10

<includeonly>http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/{{{1}}}/Documentation/{{{1}}}.xml?revision={{{2}}}&view=co</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-qtloadable-xmlurl|Models|18864}}</pre>

{{documentation/{{documentation/version}}/module-qtloadable-xmlurl|Models|18864}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-introduction-row

2018-10-19T00:48:31Z

UpdateBot: Nightly -> 4.10

<includeonly>|-
|</includeonly><noinclude>

== Usage ==

<pre>
{{documentation/{{documentation/version}}/module-introduction-start|GradientAnisotropicDiffusion}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This a row
{{documentation/{{documentation/version}}/module-introduction-row}}
This a row
{{documentation/{{documentation/version}}/module-introduction-end}}
</pre>

{{documentation/{{documentation/version}}/module-introduction-start|GradientAnisotropicDiffusion}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This a row
{{documentation/{{documentation/version}}/module-introduction-row}}
This a row
{{documentation/{{documentation/version}}/module-introduction-end}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-introduction-start

2018-10-19T00:48:31Z

UpdateBot: Nightly -> 4.10

<includeonly>{|
</includeonly><noinclude>

== Usage ==

<pre>
{{documentation/{{documentation/version}}/module-introduction-start|GradientAnisotropicDiffusion}}
{{documentation/{{documentation/version}}/module-introduction-row}}
* Some text
* More text
{{documentation/{{documentation/version}}/module-introduction-row}}
Something else
{{documentation/{{documentation/version}}/module-introduction-end}}
</pre>

{{documentation/{{documentation/version}}/module-introduction-start|GradientAnisotropicDiffusion}}
{{documentation/{{documentation/version}}/module-introduction-row}}
* Some text
* More text
{{documentation/{{documentation/version}}/module-introduction-row}}
Something else
{{documentation/{{documentation/version}}/module-introduction-end}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-header

2018-10-19T00:48:30Z

UpdateBot: Nightly -> 4.10

<includeonly>{{Clear}}{{TOC right}}{{documentation/{{documentation/version}}/header}}</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-header}}</pre>

{{documentation/{{documentation/version}}/module-header}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-introduction-end

2018-10-19T00:48:30Z

UpdateBot: Nightly -> 4.10

<includeonly>|}</includeonly><noinclude>

== Usage ==

<pre>
{{documentation/{{documentation/version}}/module-introduction-start|GradientAnisotropicDiffusion}}
{{documentation/{{documentation/version}}/module-introduction-row}}
* Some text
* More text
{{documentation/{{documentation/version}}/module-introduction-row}}
Something else
{{documentation/{{documentation/version}}/module-introduction-end}}
</pre>

{{documentation/{{documentation/version}}/module-introduction-start|GradientAnisotropicDiffusion}}
{{documentation/{{documentation/version}}/module-introduction-row}}
* Some text
* More text
{{documentation/{{documentation/version}}/module-introduction-row}}
Something else
{{documentation/{{documentation/version}}/module-introduction-end}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-introduction-logo-gallery

2018-10-19T00:48:30Z

UpdateBot: Nightly -> 4.10

<includeonly>
{{Gallery
|height=100
|lines=2
|align=center
|{{{1|}}}|{{{2|}}}
|{{{3|}}}|{{{4|}}}
|{{{5|}}}|{{{6|}}}
|{{{7|}}}|{{{8|}}}
|{{{9|}}}|{{{10|}}}
|{{{11|}}}|{{{12|}}}
|{{{13|}}}|{{{14|}}}
}}</includeonly><noinclude>

== Usage ==

<pre>
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|longname|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|Image:ITK logo.png|Some longer text to test if it wraps with a scrollbar or not.
}}
</pre>

{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
|Image:ITK logo.png|Some longer text to test if it wraps with a scrollbar or not.
}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-documentation-header

2018-10-19T00:48:29Z

UpdateBot: Nightly -> 4.10

#REDIRECT [[Template:Documentation/4.0/module-header]]

Template:Documentation/4.10/module-footer

2018-10-19T00:48:29Z

UpdateBot: Nightly -> 4.10

<includeonly>[[Category:Documentation/{{documentation/version}}/Modules|{{documentation/modulename}}]]
{{#if: {{documentation/{{documentation/version}}/module-category}} | 
[[Category:Documentation/{{documentation/version}}/Modules/{{Strloc_prefix|{{documentation/{{documentation/version}}/module-category}}|strloc= {{strfind_short|{{documentation/{{documentation/version}}/module-category}}|.|1|lenstr={{strlen_quick|{{documentation/{{documentation/version}}/module-category}}}}|}}-1}}|{{documentation/modulename}}]]
[[Category:Documentation/{{documentation/version}}/Modules/{{documentation/{{documentation/version}}/module-category}}|{{documentation/modulename}}]]
| }}</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-footer}}</pre>



[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-description

2018-10-19T00:48:28Z

UpdateBot: Nightly -> 4.10

<includeonly>{{#get_web_data:
url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/ModulesMetadata}}
|format=CSV with header
|data=xmldescriptionurl=XMLDescriptionURL
|filters=Name={{documentation/modulename}}
}}{{#xsl: https://gist.github.com/jcfr/1303051/raw/e17d031e20507f64ef86cd17dc993722a693b504/slicer-4.0-module-description.xsl | {{#external_value:xmldescriptionurl}} | parse=true | nocache = false}}</includeonly><noinclude>

== Usage ==

{{pre2|scroll|<nowiki>{{documentation/{{documentation/version}}/module-description}}</nowiki>}}

{{note}}Since this template is not specific to a given module. Exercising the template would return an empty string.

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-developerinfo

2018-10-19T00:48:28Z

UpdateBot: Nightly -> 4.10

<includeonly>{{ambox
| type = {{{amboxType|protection}}}
| image = {{{image|[[File:InProgress.png|40px|alt=Work in progress]]}}}
| text = {{{text|Section under construction.}}}
}}


</includeonly><noinclude>
__NOTOC__

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-developerinfo|Image Guided Therapy|text=Image Guided Therapy|image=[[File:Logo-IGT-i.png]]|amboxType=notice|type=CLI|category=Filtering}}</pre>

{{documentation/{{documentation/version}}/module-developerinfo
| Image Guided Therapy
| text=Image Guided Therapy
| image=[[File:Logo-IGT-i.png]]
| amboxType=notice
| type=CLI
| category=Filtering}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-developerinfo-UIowa

2018-10-19T00:48:28Z

UpdateBot: Nightly -> 4.10

<includeonly>
{{documentation/{{documentation/version}}/module-developerinfo
| {{{1}}}
| amboxType = notice
| image = [[Image:UIowaDome-Medium.gif|40px|Iowa Dome]]
| category ={{{2}}}
| text = {{{3}}}
}}
</includeonly>

<noinclude>
__NOTOC__

Template for BRAINS (and other University of Iowa) developer info section.

== Usage ==
Inputs:
<li> Module name
<li> Category
<li> Text

<pre>{{documentation/{{documentation/version}}/module-developerinfo-UIowa | BRAINSFit | Registration | See above text.}}</pre>

{{documentation/{{documentation/version}}/module-developerinfo-UIowa
| BRAINSFit
| Registration
| See above text.}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-acknowledgements

2018-10-19T00:48:27Z

UpdateBot: Nightly -> 4.10

<includeonly>{{#get_web_data:
url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/ModulesMetadata}}
|format=CSV with header
|data=xmldescriptionurl=XMLDescriptionURL
|filters=Name={{documentation/modulename}}
}}{{#xsl: https://gist.github.com/jcfr/1303070/raw/a6ee3e2f5941af30ff8aed09692317c245df1423/slicer-4.0-module-acknowledgements.xsl | {{#external_value:xmldescriptionurl}} | parse=true | nocache = false}}</includeonly><noinclude>

== Usage ==

{{pre2|scroll|<nowiki>{{documentation/{{documentation/version}}/module-acknowledgements}}</nowiki>}}

{{note}}Since this template is not specific to a given module. Exercising the template would return an empty string.

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/module-category

2018-10-19T00:48:27Z

UpdateBot: Nightly -> 4.10

<includeonly>{{#get_web_data:
url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/ModulesMetadata}}
|format=CSV with header
|data=xmldescriptionurl=XMLDescriptionURL
|filters=Name={{documentation/modulename}}
}}{{#xsl: https://gist.github.com/jcfr/1303055/raw/e4b7c9d7881d682e0283e001f3d48bd770f33593/slicer-4.0-module-category.xsl | {{#external_value:xmldescriptionurl}} | parse=true | nocache = false}}</includeonly><noinclude>

== Usage ==

{{pre2|scroll|<nowiki>{{documentation/{{documentation/version}}/module-category}}</nowiki>}}

{{note}}Since this template is not specific to a given module. Exercising the template would return an empty string.

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/extension-footer

2018-10-19T00:48:26Z

UpdateBot: Nightly -> 4.10

<includeonly>[[Category:Documentation/{{documentation/version}}/Extensions|{{documentation/modulename}}]]</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/extension-footer}}</pre>



[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/extension-section

2018-10-19T00:48:26Z

UpdateBot: Nightly -> 4.10

<includeonly>= {{{1}}} =</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/extension-section|Awesome stuff}}</pre>

{{documentation/{{documentation/version}}/extension-section|Awesome stuff}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/header

2018-10-19T00:48:26Z

UpdateBot: Nightly -> 4.10

<includeonly>__NOTOC__</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/header}}</pre>

{{documentation/{{documentation/version}}/header}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/doxygen-base-url

2018-10-19T00:48:25Z

UpdateBot: Nightly -> 4.10

<includeonly>http://slicer.org/doc/html/</includeonly><noinclude>

== Usage ==

<pre>{{documentation/{{documentation/version}}/doxygen-base-url}}</pre>

{{documentation/{{documentation/version}}/doxygen-base-url}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/doxygen-class-url

2018-10-19T00:48:25Z

UpdateBot: Nightly -> 4.10

<includeonly>{{documentation/{{documentation/version}}/doxygen-base-url}}class{{{1}}}{{#if: {{{2|}}}|-{{{2}}}|}}.html</includeonly><noinclude>

== Usage ==

=== Version specific templates ===

<pre>[{{documentation/{{documentation/version}}/doxygen-class-url|vtkMRMLNode}} vtkMRMLNode]</pre>
[{{documentation/{{documentation/version}}/doxygen-class-url|vtkMRMLNode}} vtkMRMLNode]

<pre>[{{documentation/{{documentation/version}}/doxygen-class-url|vtkMRMLNode}} here]</pre>
[{{documentation/{{documentation/version}}/doxygen-class-url|vtkMRMLNode}} here]

<pre>{{documentation/{{documentation/version}}/doxygen-class-url|vtkMRMLNode|members}}</pre>
{{documentation/{{documentation/version}}/doxygen-class-url|vtkMRMLNode|members}}

=== Version independent templates ===

<pre>[{{doxygen-class-url|vtkMRMLNode}} vtkMRMLNode]</pre>
[{{doxygen-class-url|vtkMRMLNode}} vtkMRMLNode]

<pre>[{{doxygen-class-url|vtkMRMLNode}} here]</pre>
[{{doxygen-class-url|vtkMRMLNode}} here]

<pre>{{doxygen-class-url|vtkMRMLNode|members}}</pre>
{{doxygen-class-url|vtkMRMLNode|members}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/extension-developerinfo

2018-10-19T00:48:25Z

UpdateBot: Nightly -> 4.10

<includeonly>{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = Section under construction.
}}
</includeonly><noinclude>
__NOTOC__

== Usage ==

<pre>{{documentation/{{documentation/version}}/module-developerinfo}}</pre>

{{documentation/{{documentation/version}}/module-developerinfo}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/Developers/random-image

2018-10-19T00:48:24Z

UpdateBot: Nightly -> 4.10

<includeonly>{{#get_web_data:
url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/Developers/ImageGallery/Data}}
|format=CSV with header|data=category=Category,name=Name,caption=Caption
|filters=Id={{#expr: {{CURRENTTIMESTAMP}} mod 31}}}}
[[File:{{#external_value:name}}|thumb|x150px|{{#external_value:caption}} 
[[Documentation/{{documentation/version}}/Developers/ImageGallery|Browse the image gallery]]]]</includeonly><noinclude>

== Usage ==

{{pre2|scroll|<nowiki>{{documentation/{{documentation/version}}/Developers/random-image}} </nowiki>}}

{{documentation/{{documentation/version}}/Developers/random-image}}

[[Category:Templates|{{PAGENAME}}]]
[[Category:Templates:Documentation/{{documentation/version}}|{{PAGENAME}}]]
</noinclude>

Template:Documentation/4.10/documentation-section

2018-10-19T00:48:24Z

UpdateBot: Nightly -> 4.10

#REDIRECT [[Template:Documentation/4.0/module-section]]

Documentation/4.10/WikiCheatSheet

2018-10-19T00:48:23Z

UpdateBot: Nightly -> 4.10

= Wiki templates =

== Version ==

* [[Template:Documentation/prevversion|Documentation/prevversion]] : <code><nowiki>{{documentation/prevversion}}</nowiki></code>

* [[Template:Documentation/nextversion|Documentation/nextversion]] : <code><nowiki>{{documentation/nextversion}}</nowiki></code>

* [[Template:Documentation/currentversion|Documentation/currentversion]]: Should be used outside namespaced wiki pages.

* [[Template:Documentation/version|Documentation/version]] : <code><nowiki>{{documentation/version}}</nowiki></code> : Should be used only from namespaced wiki pages.

Example of namespaced wiki pages:
* [[Documentation/Nightly/Developers/Tutorials/DocumentExtension#Naming_conventions]]
* [[Documentation/4.4/Developers]]

Example of NON namespaced wiki page:
* [[{{FULLPAGENAME}}]]
* [[Slicer4:VisualBlog]]

== Status ==

* [[Template:New|New]] : <code><nowiki>{{new}}</nowiki></code>

* [[Template:Updated|Updated]] : <code><nowiki>{{updated}}</nowiki></code>

* [[Template:Done|Done]] : <code><nowiki>{{done}}</nowiki></code>

* [[Template:Not Done|Not Done]] : <code><nowiki>{{not done}}</nowiki></code>

* [[Template:Wip|Wip]] : <code><nowiki>{{wip}}</nowiki></code>

== Highlights ==

* [[Template:Note|Note]] : <code><nowiki>{{note}}</nowiki></code>

* [[Template:Remark|Remark]] : <code><nowiki>{{remark|green|This is something awesome you should read}}</nowiki></code>

== Banners ==

* [[Template:Documentation/banner|Documentation/banner]] : <code><nowiki>{{documentation/banner}}</nowiki></code>

== Formatting ==

* [[Template:Pre2|Pre2]]: : <code><nowiki>{{pre2|Some long text}}</nowiki></code> : Similar to <code><pre></code> tag but include a horizontal scroll bar

== Images ==

* [[Template:octicon/bookmark|octicon/bookmark]] : <code><nowiki>{{octicon/bookmark|Documentation/Nightly/Developers/Build_Instructions}}</nowiki></code>

* [[Template:Tool]] : <code><nowiki>[[{{tool|logo|cdash}}|x50px]] </nowiki></code>

= Version specific wiki templates =

To learn more about documentation version (or namespace), see [[Documentation/{{documentation/version}}/Developers/Tutorials/DocumentModule#Documentation_version|here]]

== Version ==

* [[Template:Documentation/version|Documentation/version]]

* [[Template:Documentation/subpathwithoutversion|Documentation/subpathwithoutversion]]

* [[Template:Documentation/versioncheck|Documentation/versioncheck]]

== Doxygen ==

* [[Template:Documentation/{{documentation/version}}/doxygen-class-url|Documentation/{{documentation/version}}/doxygen-class-url]]

* [[Template:Documentation/{{documentation/version}}/doxygen-base-url|Documentation/{{documentation/version}}/doxygen-base-url]]

= Visual editing =
== Table ==
* Table generator: http://www.tablesgenerator.com/mediawiki_tables

Documentation/4.10/module-cli-category

2018-10-19T00:48:23Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
#REDIRECT [[Template:Documentation/4.0/module-cli-category]]

Documentation/4.10/Training

2018-10-19T00:48:22Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
=Introduction: Slicer {{documentation/version}} Tutorials=

*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
*For questions related to the Slicer4 Training Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D., Director of Training of 3D Slicer.]'''

* Some of these tutorials are based on older releases of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.

__TOC__

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome-tutorial_Slicer4.5.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want a general introduction to the software.
*Modules: Welcome to Slicer, Sample Data
*Based on: 3D Slicer version 4.6
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|width="100%"
|
*The [[media:Slicer4.5minute_SoniaPujol.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.5.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*Modules: Welcome to Slicer, Models
*Based on: 3D Slicer version 4.5
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
|align="right"|
[[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
|}

==Slicer4 Data Loading and 3D Visualization ==
{|width="100%"
|

* Slicer 4.10
** The [http://slicer.kitware.com/midas3/download/item/356408/20180430_DataLoadingAndVisualizationTutorial.pdf Data loading and visualization] ([http://slicer.kitware.com/midas3/download/item/356409/20180430_DataLoadingAndVisualizationTutorial.pptx pptx]) course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.10.
** Author: Csaba Pinter
** Modules: Welcome to Slicer, Data, Volume Rendering, Models.
** Audience: End-users
** Based on: 3D Slicer version 4.10
** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain.

* Slicer 4.5
** The [[Media:3DDataLoadingandVisualization_Slicer4.5_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.5.
** Author: Sonia Pujol, Ph.D.
** Modules: Welcome to Slicer, Sample Data, Models.
** Audience: End-users
** Based on: 3D Slicer version 4.5
** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain.
|align="right"|
[[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|250px|]]
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
|}

=Tutorials for software developers=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [https://www.dropbox.com/s/wrhrvvmplosiis1/Slicer4_ProgrammingTutorial_SPujol-SPieper_Nightly.pdf?dl=0# Slicer Programming tutorial] guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*Based on: 3D Slicer version 4.7
*The [https://www.dropbox.com/s/6yxu8qepmvywk0n/HelloPython_Nightly.zip?dl=0 HelloPython dataset] contains sample data set (MR scan of the brain) and complete Python module examples.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]

==Developing and contributing extensions for 3D Slicer==
{|width="100%"
|
*The [http://goo.gl/IP4cdg Developing and contributing extensions for 3D Slicer tutorial ] is an introduction to the internals of 3D Slicer and the process of contributing a 3D Slicer extension.
*Authors: Andrey Fedorov, Jean-Christophe Fillion-Robin, Steve Pieper
*Audience: Developers
*Based on: 3D Slicer version 4.4
|align="right"|
[[Image:Contributing3DSlicerExtension.png|right|250px|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|width="100%"
|
*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/DiffusionMRIanalysis.pdf Diffusion Tensor Imaging Tutorial] course guides through the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts.
*Author: Sonia Pujol, Ph.D.
*Audience: End-users and developers
*Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups,Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.6
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
|align="right"|
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
|}

==Slicer4 Neurosurgical Planning Tutorial==
{|width="100%"
|
*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
*The [http://dmri.slicer.org/tutorials/neurosurgical_planning_dti Neurosurgical Planning tutorial] course guides through the generation of fiber tracts in the vicinity of a tumor.
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
*Audience: End-users and developers
*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.6
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DSlicer_Dicom_RSNA2015_SoniaPujol.pdf |3D Visualization of DICOM images for Radiology Applications]] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
*Modules: DICOM, Volumes, Volume Rendering, Models.
*Based on: 3D Slicer version 4.5
*The [[Media:3DVisualization_DICOM_images_part1.zip‎ | 3DVisualizationDICOM_part1]] and [[Media:3DVisualization_DICOM_images_part2.zip | 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
|align="right"|
[[Image:Slicer4RSNA_2.png|right|250px|]]
|}

==Slicer4 Quantitative Imaging tutorial==
{|width="100%"
|
*The [[media:QuantitativeImaging_Slicer4.5.pdf‎ | Slicer4 Quantitative Imaging tutorial]] guides through the use for Slicer for quantifying small volumetric changes in slow-growing tumors, and for calculating Standardized Uptake Value (SUV) from PET/CT data.
*Authors: Sonia Pujol, Ph.D., Katarzyna Macura, M.D., Ron Kikinis, M.D.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
*Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
*Based on: 3D Slicer version 4.5
*The [[media:QuantitativeImaging.zip‎| Quantitative Imaging dataset]] contains a series of MR and PET/CT data.
|align="right"|
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
|}

== Slicer4 IGT ==
{|width="100%"
|
*[http://www.slicerigt.org/wp/user-tutorial/ Slicer IGT tutorials]
*Authors: Tamas Ungi, M.D, Ph.D., Junichi Tokuda, Ph.D.
*Audience: End-users interested in using Slicer for real-time navigated procedures. E.g. navigated needle insertions or other minimally invasive medical procedures.
*Modules: SlicerIGT Extension
*Based on: Slicer4.3.1-2014.09.14
*Data: [https://onedrive.live.com/redir?resid=7230D4DEC6058018!2937&authkey=!AGQkSCZOwjVYXw8&ithint=folder%2cpptx Slicer-IGT datasets]
|align="right"|
[[Image:SlicetIGT.png|right|150px|]]
|}

== Slicer4 Image Segmentation ==

{|width="100%"
|
* Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
** '''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia.
** '''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc
** Audience: Users and developers interested in segmentation and 3D printing
** Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
** Based on: 3D Slicer version 4.7
|align="right"|[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]]
|---
|
* '''[https://youtu.be/BJoIexIvtGo Video tutorial: Whole heart segmentation from cardiac CT]''' shows how to use the Segment Editor module for segmenting heart ventricles, atria, and great vessels from cardiac CT volumes.
** Author: Andras Lasso, PhD
** Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation.
** Sample data set: http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd
** Based on: 3D Slicer version 4.8
|align="right"|[[Image:WholeHeartSegYoutube.png|280px]]
|---
|
* '''[https://youtu.be/0at15gjk-Ns Video tutorial: Femur and pelvis segmentation from CT]''' shows how to use the Segment Editor module for segmenting pelvis and femur from CT volumes.
** Author: Andras Lasso, PhD
** Audience: Users who need to segment bones in CT images for visualization, quantification, or simulation.
** Sample data set: https://wiki.cancerimagingarchive.net/display/Public/TCGA-PRAD (Subject TCGA-VP-A878)
** Based on: 3D Slicer version 4.8
|align="right"|[[Image:FemurSegmentationYoutube.png|280px]]
|---
|
* [https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes]
|}

== Slicer4 Image Registration ==

{|width="100%"
|
*The [https://www.slicer.org/slicerWiki/index.php/File:RegistrationTutorial_3DSlicer4.5_spujol.pdf Registration tutorial] shows how to perform intra- and inter-subject registration within Slicer.
* Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
* Audience: Users and developers interested in image registration
* Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
|align="right"|[[File:registration_Slicer4.png|250px]]
|}
*Based on: 3D Slicer version 4.5
See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].

==Slicer4 Radiation Therapy Tutorial ==

{|width="100%"
|
* The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
* Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
* Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
* Based on Slicer 4.7
|align="right"|

|}

== DICOM ==

{|width="100%"
|
* DICOM export: '''[https://youtu.be/nzWf4xHy1BM Export CT and segmentation to DICOM - video tutorial]'''
* Author: Andras Lasso, Csaba Pinter.
* Dataset: CTChest sample data in Slicer.
* Based on Slicer 4.9
|align="right"|

|}

== Other ==

Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on [http://www.youtube.com/results?search_query=3d+slicer&sm=3 You Tube].

= 3D Slicer Tutorial contests=

==Winter 2017 Tutorial contest==

===Segmentation for 3D printing===
{|width="100%"
|
*The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] ([https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx pptx]) is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module, demonstrated through the popular topic of 3D printing.
*Author: Csaba Pinter (Queen's University, Canada)
* [https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube].
*Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
|align="right"|
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
|}

===Slicer Pathology===
{|width="100%"
|
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
*Dataset: Available directly with the Slicer Pathology Slicer extension.
|align="right"|
[[File:SlicerPathologyScreenShot8.png | 200px]].
|}

===Simple Python Tool for Quality Control of DWI data===
{|width="100%"
|
*The [http://www.na-mic.org/Wiki/images/3/3a/SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from nifti file format (separated bvecs, bvals files).
*Author: Laurent Chauvin (ETS Montreal)
*Dataset: Not available.
|align="right"|
[[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].
|}

===SPHARM-PDM===
{|width="100%"
|
*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
*Dataset: [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
|align="right"|
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
|}

===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
{|width="100%"
|
*The [https://www.na-mic.org/Wiki/images/a/ab/ROSIGTLTutorial_Tokuda_Jan2017.pptx Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] describes the software architecture of surgical robot systems and allows to acquire hands-on experience of software-hardware integration for medical robotics.
*Author: Junichi Tokuda (Brigham and Women’s Hospital)
*Dataset: Not available.
|align="right"|
[[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].
|}

===Fiber Bundle Volume Measurement===
{|width="100%"
|
*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
*Dataset: [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]] and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).
|align="right"|
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
|}

==Winter 2016 Tutorial contest==

===Subject Hierarchy===
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/2/27/SubjectHierarchy.TutorialContestWinter2016.pdf Subject Hierarchy] tutorial demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset.
*Author: Csaba Pinter, Queen's University, Canada
*Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip SlicerRT_WorldCongress_TutorialIGRT_Dataset] The tutorial dataset is a two-timepoint phantom dataset taken from a RANDO head&neck phantom. It contains two studies, the planning one is a DICOM study consisting of a CT grayscale image and radiotherapy data: contours, dose distribution, treatment beams, plan information. The second timepoint consists of a CT NRRD volume and a dose NRRD volume.
|align="right"|
[[File:SubjectHierarchyTutorial.png | 200px]].
|}

===Fiber Bundle Selection and Scalar Measurements===
{|width="100%"
|
*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/FiberBundleSelectionAndScalarMeasurement.pdf Fiber Bundle Selection and Scalar Measurements] tutorial guides through the use of the Diffusion Bundle Selection module and the Fiber Tract Scalar Measurement module for diffusion MRI tractography data analysis.
*Author: Fan Zhang, University of Sydney Australia and Brigham and Women's Hospital
*Dataset: [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip| Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]]
|align="right"|
[[File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016_Snapshot.png|200px]]
|}

===Plastimatch ===
{|width="100%"
|
*The [http://www.na-mic.org/Wiki/images/5/5c/Plastimatch_TutorialContestWinter2016.pdf Plastimatch tutorial] guides through registration and wrapping of DICOM and DICOM-RT data using the Plastimatch extension of 3D Slicer.
*Author: Gregory Sharp, Massachusetts General Hospital
*Dataset: [http://www.na-mic.org/Wiki/index.php/File:Plastimatch_TutorialContestWinter2016.zip Plastimatch Tutorial Dataset]
|align="right"|
[[File:PlastimatchTutorial_Winter2016Contest.png|200px]]
|}

===UKF ===
{|width="100%"
|
*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/UKFTractography.pdf UKF tutorial] guides through the use of the Unscented Kalman Filter (UKF) tractography module.
*Author: Pegah Kahali, Brigham and Women's Hopital
*Dataset: [http://www.na-mic.org/Wiki/index.php/File:UKF-Tractography_TutorialContestWinter2016.zip UKF tutorial Dataset]
|align="right"|
[[File:UKF_Winter2016.png|200px]]
|}

==Summer 2014 Tutorial contest==

===Cardiac Agatston Tutorial===
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf Cardiac Agatston Scoring Tutorial]
*Authors: Jessica Forbes, Hans Johnson, University of Iowa
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip Cardiac Agatston Scoring Tutorial Dataset]
|align="right"|
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
|}

===CMR Toolkit LA workflow===
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf CMR Toolkit LA Workflow Tutorial]
*Authors: Salma Bengali, Josh Cates, University of Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
|align="right"|
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
|}

==Summer 2013 Tutorial contest==

===Cardiac MRI Toolkit===
{|width="100%"
|
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
*Authors: Salma Bengali, Josh Cates, SCI, Utah
*Dataset: [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
|align="right"|
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
|}

===HelloCLI===
{|width="100%"
|
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
*Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
|align="right"|
[[Image:Cli_icon.png|300px]]
|}

===SlicerRT===
{|width="100%"
|
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
*Authors: Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
*Dataset: [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
|align="right"|
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
|}

===DTIPrep===
{|width="100%"
|
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
*Authors: Dave Welch, SINAPSE, IOWA
*Dataset: [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
|align="right"|
[[Image:DTIPrep-tutorial.png|250px]]
|}

== Summer 2012 Tutorial contest ==

===Automatic Left Atrial Scar Segmenter ===
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
*Authors: Greg Gardner, Josh Cates, SCI, Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
|align="right"|
[[Image:Carma afib auto scar.png|250px]]
|}

===Qualitative and quantitative comparison of two RT dose distributions===
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions]
*Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH
|align="right"|
[[Image:PlastimatchDose.png|250px]]
|}

===Dose accumulation for adaptive radiation therapy===
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
*Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
|align="right"|
[[Image:AdaptiveradiationTherapy.png|250px]]
|}

===WebGL Export===
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf WebdGLExport]
*Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
|align="right"|
[[Image:WebGLExport.png|250px]]
|}

===OpenIGTLink===
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
[[Image:OpenIGTLink.png|250px]]
|}

=Additional resources =
{|width="100%"
|
* This ''Slicer 4.1 [http://vimeo.com/41096643 webinar]'' presents the new features and improvements of the release, and a brief overview of work for the next release.
* Authors: Steve Pieper Ph.D.
* Audience: First time users and developers interested in Slicer 4.1 new features.
* Length: 0h20m
|align="right"|[[Image:Webinar-Slicer-4.1.png|250px]]
|}
 
----
 
{|width="100%"
|
*This ''Intro to Slicer 4.0 [http://vimeo.com/37671358 webinar]'' provides an introduction to 3DSlicer, and demonstrates core functionalities such as loading, visualizing and saving data. Basic processing tools, including manual registration, manual segmentation and tractography tools are also highlighted. This webinar is a general overview. For in depth information see the modules above and the documentation pages.
*Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S.
*Audience: First time users interested in a broad overview of Slicer’s features and tools.
*Length: 1h20m
|align="right"|[[Image:Webinar.png|250px]]
|}
 
----
 
{|width="100%"
|
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself.
:Author: Dominik Meier, Ph.D.
:Audience: users interested learning/applying Slicer image registration technology
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
|}

= External Resources =

== Resources for Chinese users ==

{|width="100%"
|
A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text.

* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗]

* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247484787&idx=1&sn=1f6279bdccab168fc79b7275e9fe91ca&chksm=eacc0f41ddbb8657be92f617661133d87bb55a4ecf12f786e97a8b7d5249a05d11e0cd620c3f#rd distal anterior cerebral artery aneurysm 3D Slicer：漂亮得不像实力派]

* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486360&idx=1&sn=f833b13a26f543aa9175419a03df7f52&chksm=eacc01aaddbb88bcb004773a4db8a9b3c7633d21cda3956f84b96515252eb861c5eb1e75a60b&mpshare=1&scene=24&srcid=0212LIfOkBRm9CvA7ImHCpRt#rd meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案]

* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486079&idx=1&sn=9b926dc398a408e3441082b9e0ffde61&chksm=eacc004dddbb895bf9b60f5f1bc443513196e4cb90a6caf6f348a4da7b7fc22eb658661aeb49&mpshare=1&scene=24&srcid=0212AFtT2Wq7K7bvkMGTdyih#rd Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法（五 ]

* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247485356&idx=1&sn=044f5899b651b35994db00c32ab688ee&chksm=eacc0d9eddbb8488f16ff82bb1dda8456a4011790fed024781972d578783e67781443cf4a319&mpshare=1&scene=24&srcid=0212G45TadrPnX8tp9eaNXUs#rd Hematoma modeling 血肿建模的第11种方法]

* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索]

|align="right"|
[[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]]
|}

== Resources in German ==

* [https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles)

== Murat Maga's blog posts about using 3D Slicer for biology ==

* [https://blogs.uw.edu/maga/2017/04/11/getting-started-with-3d-slicer-as-a-biologist/ Slicer for Biologists]
* [https://blogs.uw.edu/maga/2017/04/11/a-worked-example-getting-and-visualizing-data-from-digimorph/ Loading data from DigiMorph]
* [https://blogs.uw.edu/maga/2017/04/11/morphosource-data-and-dealing-with-dicom-series-in-slicer/ Fixing problem DICOM]
* [https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesom]

== Using the (legacy) Editor ==

=== Fast GrowCut ===

{|width="100%"
|
* The [[media:FastGrowCutTutorial.pdf |Fast GrowCut tutorial]] shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
* Authors: Hillary Lia
* Audience: Users interested in segmentation
|align="right"|[[File:FastGrowCutLogo.png|200px]]
|}

=== Use case: Slicer in paleontology ===

This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field:

* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-ii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part II]
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part III]
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iv.html Open Source Paleontologist: 3D Slicer: The Tutorial Part IV]
* [http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-v.html Open Source Paleontologist: 3D Slicer: The Tutorial Part V]
* [http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI]

== Team Contributions ==
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].

== User Contributions ==
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.

[http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]

Documentation/4.10/Training/UserContributions

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== Demonstration videos on YouTube ==

=== Slicer3: How to load data and make models ? ===
{|width="100%"
|
* [http://www.youtube.com/watch?v=GNsWRnm7gQw&context=C42d9859ADvjVQa1PpcFPhXz87xj_xyVq19zSUexfAbEm8Iz3DYEk= Narrated screencast video] showing how to load data and make models.
* Author: John Muschelli
* Dataset: NA
* Based on Slicer 3
|align="right"|

|}

===Prostate segmentation using Segment Editor===

* https://www.slicer.org/w/images/0/0f/SlicerProstate_Workflow6.26.2018.pdf
* Author: Nicole Wake, NYU Langone
* Based on Slicer 4

Documentation/4.10/SlicerApplication/SupportedDataFormat

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=File formats supported by Slicer {{documentation/version}}=
{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!Format
!File Name Extensions
!Read
!Write
!Module
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Scenes
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Data|Data]]
|-
| MRML (Medical Reality Markup Language File)
| .mrml
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|MRML file is a xml-formatted text file with scene metadata and pointers to externally stored data files. See [[Documentation/{{documentation/version}}/Developers/MRML|Data Model]]. Coordinate system: RAS
|-
| MRB (Medical Reality Bundle)
| .mrb, .zip
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes (.mrb extension only)
|MRB is a binary format encapsulating all scene data (bulk data and metadata). Internally it uses zip format. Any .zip file that contains a self-contained data tree including a .mrml file can be opened. Coordinate system: RAS
|-
| Slicer 2 Scene
| .xml
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
| xml-formatted text file with scene metadata and pointers to externally stored data files. Coordinate system: RAS
|-
| Data collections in XNAT Catalog format (".xcat") or XNAT Archive format (".xar")
| .xcat
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
| Data collections in XNAT Archive format (".xar")
| .xar
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Raster Images ''this includes 2D and 3D images, and more complicated types such as DWI or DTI''
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]]
|-
| [http://medical.nema.org/ DICOM]
| .dcm ...
|bgcolor="LightGreen" align="center"|yes<ref>For a number of dMRI formats we recommend use of the [[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|DICOM to NRRD converter]] before loading the data into Slicer.</ref>
|bgcolor="LightGreen" align="center"|yes (some data types)<ref>Image volumes, RT structure sets, dose volumes, etc. can be exported using [[Documentation/{{documentation/version}}/Modules/DICOM#DICOM_export|DICOM module's export feature]]. Limited support for writing image volumes in DICOM format is provided by the [[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] module. Support of writing DICOM Segmentation Objects is provided by the [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting extension]]</ref>
|[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]], [[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|DICOMToNRRDConverter]], [[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|CreateDICOMSeries]], [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting extension]]. Coordinate system: LPS (specified by the DICOM standard)
|-
| [http://teem.sourceforge.net/nrrd/format.html NRRD]
| .nrrd, .nhdr
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: as defined in the file header (usually LPS)
|-
| [http://www.itk.org/Wiki/MetaIO/Documentation MetaImage]
| .mhd, .mha
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: LPS<ref>According to [http://www.itk.org/Wiki/Proposals:Orientation#Current_ITK_Usage_and_sources_of_confusion MetaIO naming scheme] DICOM 'LPS' direction is 'RAI'.</ref> (AnatomicalOrientation in the file header is ignored)
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK]
| .vtk
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: LPS
|-
| [http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm Analyze]
| .hdr, .img, .img.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| [http://nifti.nimh.nih.gov/nifti-1/ NifTI]
| .nia, .nii, .nii.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| BMP
| .bmp
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| BioRad
| .pic
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Brains2
| .mask
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| GIPL
| .gipl .gipl.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| JPEG
| .jpg, .jpeg
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| LSM
| .lsm
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| PNG
| .png
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Stimulate
| .spr
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| TIFF
| .tif, .tiff
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| MGH-NMR
| .mgz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| [http://en.wikipedia.org/wiki/MRC_(file_format) MRC] Electron Density
| .mrc, .rec
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Models
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Models|Models]]
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK Polygonal Data]
| .vtk
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Polygonal Data]
| .vtp
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK Unstructured Grid Data]
| .vtk
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| [http://www.vtk.org/VTK/img/file-formats.pdf VTK XML Unstructured Grid Data]
| .vtp
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| STL
| .stl
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| OBJ
| .obj
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| Freesurfer
| .orig, .inflated, .sphere, .white, .smoothwm, .pial
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
| Others (to be tested)
| .g, .byu
|bgcolor="LightGreen" align="center"|yes
|bgcolor="#f34a33" align="center"|no
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Fiducials
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Markups|Markups]]
|-
| CSV
| .fcsv
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"|Rulers
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]]
|-
| CSV
| .acsv
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| Coordinate system: RAS
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transforms
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]]
|-
| [http://www.itk.org/ItkSoftwareGuide.pdf ITK Transform]
| .h5
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| For linear, b-spline, grid (displacement field), thin-plate spline, and composite transforms. Coordinate system: LPS
|-
| [http://www.itk.org/ItkSoftwareGuide.pdf ITK Transform]
| .tfm, .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| For linear, b-spline, and thin-plate spline, and composite transforms. Coordinate system: LPS
|-
| [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf Matlab MAT-File]
| .mat
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| For linear and b-spline transforms. Coordinate system: LPS
|-
| Displacement field
| .nrrd, .nhdr, .mha, .mhd, .nii, .nii.gz
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
| For grid transform. Coordinate system: LPS
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Transfer Functions
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]]
|-
| Volume Rendering properties
| .vp
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Lookup tables
! scope="col" style="border-top: 1px solid grey;"| [[Documentation/{{documentation/version}}/Modules/Colors|Colors]]
|-
| [[Documentation/{{documentation/version}}/Modules/Colors#File_format|Text]]
| .txt, .ctbl
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
! scope="col" colspan="4" style="border-bottom: 1px solid grey;border-top: 1px solid grey;"| Double Arrays
! scope="col" style="border-top: 1px solid grey;"|
|-
| CSV
| .mcsv
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|-
| Text
| .txt
|bgcolor="LightGreen" align="center"|yes
|bgcolor="LightGreen" align="center"|yes
|
|}

<references/>

= What if your data is not supported? =

If you have a file of binary data and you know the data is uncompressed and you know the way it is laid out in memory, then one way to load it in Slicer is to create a .nhdr file that points to the binary file.

A way to get started is to download sample data that is similar to your data (e.g. a CT or MR). Then save that data in .nhdr format and start editing the file to match your data.

Refer to the [http://teem.sourceforge.net/nrrd NRRD format documentation] to see what the keys mean.

=References=
* [http://www.vtk.org/Wiki/ITK_File_Formats ITK File Formats]


{{documentation/{{documentation/version}}/slicerapplication-footer}}

Documentation/4.10/TractographyFiducialSeeding

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{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Demian Wasserman, BWH 
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
|Image:Logo-namic.jpg|NA-MIC
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.




If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre>

If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>

Using this later template, the final syntax would be:
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>





{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1:
* Use Case 2:


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}




{{note}}The section above is generated using the following wiki code:
<pre>
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}
</pre>

If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre>

If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>

Using this later template, the final syntax would be:
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>





{{documentation/{{documentation/version}}/module-footer|category=Example}}

Documentation/4.10/SlicerApplication/Settings

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#REDIRECT [[Documentation/Nightly/SlicerApplication/ApplicationSettings]]

Documentation/4.10/SlicerApplication/StereoViewing

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=Purpose=
[[image:Slicer4StereoPanel-2011-11.png|right|The Stereo Viewing Icon]]

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic, Interlaced. These rendering modes are automatically enabled.

The final mode, called QuadBuffer, will be enabled if Slicer detects that your hardware can support it.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algorithm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue only rendering.

'''[http://en.wikipedia.org/wiki/Anaglyph_image Analglyph]''' - This algorithm uses the same glasses as the red/blue algorithm but preserves much of the natural color of rendered objects. In general, this preserves the colors in the rendered scene, but adds depth. Some "bleedthrough" still occurs between the eyes, but there are less visual artifacts compared with the red/blue algorithm.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''QuadBuffer''' - Available only when automatically detected. Formally called '''"CrysalEyes'''" named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode can enable '''"active stereo"''', '''"frame sequential stereo"''' or '''"passive stereo '''" depending on how the video drivers are configured. Only some graphics cards support OpenGL quad buffer technology such as professional graphics cards such as NVIDIA Quadro or ATI FireGL. Not all display devices support this rendering mode.


{{documentation/{{documentation/version}}/slicerapplication-footer}}

Documentation/4.10/SlicerApplication/StructureSets

2018-10-19T00:48:20Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
__NOTOC__
These are Greg's development notes. Beware of inaccurate and misleading information below.

=Introduction=

The term "structure set" is used in RT to denote a set of structures (labels) which are attached to an image.
The goal of this project is to improve Slicer so it can handle overlapping structures.
The following is a rough list of required functionality:

# Identify structureset images at load time
# Load structureset images
# Display overlapping contours in structure set
# Editor can switch between labelmap and structureset representation
# Modify editor GUI to make easier selecting current structure
# Save structureset images

=How to git=
# Basic tutorials
## http://www.slicer.org/slicerWiki/index.php/Slicer3:git-svn
## http://git.or.cz/course/svn.html
# My code is located here
## https://github.com/gregsharp/Slicer/tree/gcstest
# It is a fork of SlicerRT
## https://github.com/SlicerRt/Slicer
# Or perhaps Slicer
## https://github.com/Slicer/Slicer
# Update like this:
## git pull git@github.com:gregsharp/Slicer.git gcstest
## Or, because I created an alias, like this:
## git pull gcs gcstest
## The alias is made like this:
## git remote add gcs git@github.com:gregsharp/Slicer.git
# My code is branched off of SlicerRT
## To rebase onto main slicer trunk, do this:
## git remote add slicer https://github.com/Slicer/Slicer.git
## git pull --rebase slicer master
## However, this doesn't work because my fork contains all of SlicerRT, which conflicts with slicer
# So I make a new fork, based on slicer itself
## git clone git://github.com/Slicer/Slicer.git Slicer-gcs
## git remote add gcs-slicer git@github.com:gregsharp/gcs-slicer.git
## git push gcs-slicer master
## But this doesn't work "ERROR: Repository not found."
# Eventually I had to give up, and delete the repository
## The changes were to this file: Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx

=Notes=

# Identifying structureset images
## For now, I just assume that any vector image is a structureset image
# Loading structureset images
## Images, when loaded, are sent to vtkMRMLVolumeArchetypeStorageNode::ReadData(), which decides whether the file has a scalar or vector image
## The type of the MRML node created is vtkMRMLVectorVolumeNode
## Ref: Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx
## A vtkMRMLVectorVolumeDisplayNode is attached to the storage node
# Is an image a labelmap?
## This is apparently a function of the XML file, not the image
## vtkMRMLScalarVolumeNode::SetLabelMap()
# Labelmap display
## ??
## ??
# Displaying overlapping contours

Documentation/4.10/SlicerApplication/QtTesting

2018-10-19T00:48:19Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
{|width="100%"
|
__TOC__
|align="right"|
[[Image: 3DSlicerQtTesting.png]]
|}
=Overview=

Too lazy to do the same actions over and over? QtTesting is the answer! The QtTesting library provides you with an easy way to record and play macros with 3DSlicer. Included in this library is a user-friendly recording interface that shows you what actions you're recording as well as a simple and smart playback interface that will allow you to control actions whenever you want. With no input from the user, QtTesting record all accomplished actions from the point you have started the record until you stop it! "Create a puppet and let it do the rest ... "

Slicer developers use this library to record tutorials and test the 3D Slicer application. How to create you own [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/QtTesting QtTesting test]. 

[[Image: QtTestingMenu.png]]

{{ambox
| text = ''QtTesting is an effort started by the [http://paraview.org/Wiki/Testing_design ParaView team]''
}}

==Activate QtTesting==

{|width="100%"
|valign="top"|
By default, QtTesting is not activated. You must enable it to be able to record or play a saved macro.
* Open the [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings|Application Settings]] dialog.
* On the left side, select the ''QtTesting'' panel
* Enable QtTesting by toggling the checkbox
* Restart Slicer
|align="right"|
[[Image: QtTestingSettigns.png |450px]]
|}

==Recorder==
Recording a macro consists in observing all the high level events (or low level in some cases) that the user generate by interacting with the GUI elements. All the events are saved into a file (.xml) that can be used later to [[#Player|replay]] the recorded events in the same or different instance of the Slicer application.
{|width="100%"
|
=== How to record a macro===
* From the [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Application_Menu|menu bar]], open the ''Edit'' menu and select the ''Record Macro'' item to start recording all your following events.
''A record dialog appears at the bottom left of the application''

=== Record dialog ===
* Shows the last event recorded
* Numbers of events recorded
* ''You can stop the recording anytime by clicking on the Stop button''

=== Save macro ===
* When the recording is stopped, a dialog shows up to ask where to save the recorded macro file.

|align="right"|
[[Image: QtTestingRecorderDialog.jpg |300px]]
|}

==Player==
Recorded macros (.xml) can be replayed within Slicer sessions. Note that the success of the macro execution can depend on the original state of the application.

{|width="100%"
|
=== How to play a macro ===
# From the [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Application_Menu|menu bar]], open the ''Edit'' menu and select the ''Play Macro'' item to open the player dialog.
# Choose the xml macro that you want to play
# Press the "Play" button to start executing the macro

Slicer will ask if you want to restore the previously recorded settings. See [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting#Default_settings_recorded|below]]

=== Player dialog ===
*'''Controller widget'''
** Play, pause, stop or play-step-by-step your macro.
** ''Logs'' check button shows/hides information about played events and errors if any.
** ''Time step'' controls the playback speed by waiting Xms before playing each event.

* '''Player tab''' (''default tab'')
** Show the macro file played.

* '''Info tab''' :
** Show the last event played.

===Default settings recorded===
To limit playback problems, QtTesting records automatically some of the applications settings.
* General settings :
** The application's geometry
** The application's state
** The application's name
** The application's version

* 3DSlicer settings :
** The current layout
** The current module

Before each play back, the application might have different current settings, QtTesting then asks if you want to restore the settings to the record application state. To maximize the chance of a successful playback, settings must be restored to set the application into a state as much as possible similar to when the macro was recorded. 
{{ambox
| type = speedy
| small = left
| text = It's strongly recommended to accept !
}}

|align="right"|
[[image: QtTestintMenuPlayerback.png | 250px]]

[[image: QtTestintMacroFileDialog.png | 300px]]

[[image: QtTestintPlayererDialog.jpg | 300px]]

[[image: QtTestintRestoreSettingsDialog.png | 300px]]
|}

==User limitations==

''QtTesting in 3DSlicer is still under [[Documentation/{{documentation/version}}/Developers/QtTesting|heavy development]], some events might not be recorded properly.''

===What is subject to not work :===
* Some actions under submenus, mainly actions on widget.

===Work, but not perfectly:===
* Shifts/offsets might happen when you recording events in the 3D views.

Documentation/4.10/SlicerApplication/SavingData

2018-10-19T00:48:19Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/slicerapplication-header}}


__NOTOC__
=Introduction=

{|width=100%
|valign=top|
It is possible to save the current scene (including all scene snapshots, fiducial lists, ''etc.'') and/or individual datasets.

The "Save Data" panel is accessed through the File menu using '''File->Save''', or by using the [[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts|CTRL-S]] keyboard shortcut.

'''Note:''' in order to provide a rich set of options for saving data, the '''Save Scene and Unsaved Data''' interface does not behave in the way that Windows data explorer and Gnome file browser behave. The user is encouraged to read this documentation carefully, and be mindful when specifying save options.
<gallery widths="200px" heights="200px" perrow="4">
image:Save-mj.png|Save Icon
image:SlicerApplication-FileSave.png|File/Save
</gallery>

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Select What to Save| Select What to Save ]]
|[[#ASelect Save Destinations| Select Save Destinations ]]
|[[#Modify Filenames & Formats| Modify Filenames & Formats ]]
|[[#Supported formats|Supported formats]]
|}

=Select What to Save=
When invoked, Slicer will select the scene and any modified datasets for saving by default. This set of selections can be overridden by manipulating the checkboxes in the leftmost column. In addition to the checkbox in the '''Node Name'' column header, two buttons in the panel's upper left provide convenient selection shortcuts for commonly-used selection states arrayed in the interface:

<gallery widths="100px" heights="100px" perrow="4">
Image:SlicerApplication-SaveData-SelectSceneAndData-mj.png|Select Scene Description and Modified Data
Image:SlicerApplication-SaveData-SelectModifiedData-mj.png|Select Modified Data Only
</gallery>

=Save Options=

<gallery widths="400px" heights="200px" perrow="4">
Image:MRB-dialog-option-Screen Shot 2013-11-19 at 11.27.31 AM.png|Picking the bundle option (by clicking the wrapped package icon, third on the top row) selects the .MRB file format. MRB is Medical Reality Bundle, which puts all the content into a single file. So all volumes, models, scene options and other parts are in one convenient place.
</gallery>

=Select Save Destinations=

* Change the destination for ALL SELECTED FILES (scene description and data) by using the '''Destination for all Selected''' button at the bottom left. This button raises a directory browser and lets you choose and change the save destination for all of your selections.

* To change the save destination for an individual dataset or scene file, select the file browser icon in the '''Data Directory''' column. If the dataset or scene file was not previously selected, it will be automatically selected.

* To revert to original save destinations, just '''Cancel''' the save instead of finishing; the next time this interface is raised, the original settings will be shown.

<gallery widths="400px" heights="200px" perrow="4">
Image:SlicerApplication-SaveData.png|Before changing all destinations
Image:SlicerApplication-SaveData-DestinationsChanged.png|After changing all destinations
</gallery>

=Modify Filenames & Formats=

* Finally, you can specify the file names for the scene and data files to be saved in the '''File Name''' column. By changing the extension in this column, you can determine what file type will be used to save the data (e.g. typing <code>.nrrd</code> for instance will save the volumes in the <code>NRRD</code> format), and the '''File Format''' column will be updated appropriately. Alternatively, a different format can be selected from the menu provided in the '''File Format''' column. If the dataset whose name or format are modified was not previously selected, it will be automatically selected.

'''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.

The GUI panel is shown below:

<gallery widths="600px" heights="200px" perrow="4">
Image:SlicerApplication-SaveData.png | Save Data GUI
</gallery>

=Supported formats=
Please refer to the [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|supported data format]] page.
{{ombox
|type=content
|text=Many file formats are 'lossy' when it comes to saving and restoring image orientation metadata. For example, Analyze format cannot store all image orientations and .vtk format for images does not store orientation information at all. When exporting data to a new format, please reload the data to ensure the correct data has been saved. In general, NRRD, NIfTI, and Meta formats preserve exported information. All meta-information other than image content and image orientation (such as patient name, acquisition-related details) is lost when the image loaded from DICOM is saved into any of the non-DICOM formats!
}}

=Information for Developers=
Consider reading the [[Documentation/{{documentation/version}}/Developers/IO|Developers/IO]] page for information about programmatically loading and writing files.


{{documentation/{{documentation/version}}/slicerapplication-footer}}

Documentation/4.10/SlicerApplication/MainApplicationGUI/MouseModes

2018-10-19T00:48:18Z

UpdateBot: Nightly -> 4.10

===Mouse Modes===
[[image:Slicer4MouseModeToolbar.jpg | center]]
Slicer has two mouse modes: '''Transform''' (which allows interactive rotate, translate and zoom operations), and '''Place''' (which permits objects to be interactively placed in 3D or 2D).

The toolbar icons that switch between these mouse modes are shown from left to right above, respectively. '''Place Fiducial''' is the default place option as shown above; options to place both '''Ruler''' and '''Region of Interest''' Widgets are also available from the drop-down Place Mode menu.

'''Hint: Transform''' mode is the default interaction mode. By default, '''Place''' mode persists for one "place" operation after the Place Mode icon is selected, and then the mode switches back to Transform. Place mode can be made persistent (useful for creating multiple fiducial points, rulers, etc.) by checking the '''Persistent''' checkbox shown rightmost in the Mouse Mode Toolbar.

Documentation/4.10/SlicerApplication/MouseandKeyboardShortcuts

2018-10-19T00:48:18Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/slicerapplication-header}}


=Table of Content=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
=Mouse=
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Cross_Reference|Cross reference]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Window_.26_Level| Window Level]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Opacity_blending|Opacity Blending]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Rotate.2C_Zoom.2C_Pan|Rotate, Zoom, Pan]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Selecting_.26_Manipulating|Selecting and Manipulating]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Mouse_Modes|Mouse modes]]

|bgcolor="#CCCCCC"|
|valign="top"|

=[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Keyboard_Accelerators| Keyboard Accelerators]]=
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#General| General]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#3D_Viewer| 3D Viewer]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Slice_Viewer| Slice Viewer]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Transfer_Functions| Transfer functions]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Keyboard_Shortcuts.E2.80.94Windows| Non-Slicer Key bindings for Windows]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Keyboard_Shortcuts.E2.80.94Mac| Non-Slicer Key bindings for Mac]]
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts#Python_Interactor|Python Interactor]]
|}

=Mouse Operations=
Below is basic information about how to use the three-, two-, and one-button mouse (or trackpad) on Windows, Mac, and Linux platforms to perform basic interaction operations in Slicer:
{|
|-
|
==Cross Reference==
Holding down the Shift-Key while moving the mouse in any '''Slice Viewer''' will cause other Slice Viewers to scroll to the same position. This feature can be combined with cross-hairs.

==Crosshairs==
Crosshairs are available for precise cross-correlation between Sliceviewers. Their appearance can be changed. In '''Navigation''' mode a box at the center of the crosshair allows to center the other Sliceviewers to that location by clicking and dragging the box.

==Window & Level==
*Left-click & drag in a '''Slice Viewer''' adjusts Window / Level.
**Adjust the '''level''' by moving the mouse '''vertically'''
**Adjust the '''window''' by moving the mouse '''horizontally'''
*An interface with sliders and numeric input fields is available in the [http://www.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Modules/Volumes Volumes Module] for more precise controls.

==Opacity blending==
*Ctrl ([[image:Apple-Command.png]] on the Mac) & Left-click & drag in a '''Slice Viewer''' adjusts opacity.
**Adjust the '''foreground opacity''' by moving the mouse '''vertically'''
**Adjust the '''labelmap opacity''' by moving the mouse '''horizontally'''
*An interface with sliders and numeric input fields is available in the Slice View Controller for more precise controls.

|[[image:2011-12-Crosshair-Toolbar.png|150px|thumb|Crosshair-Toolbar A variety of crosshair modes are available in Slicer]]
|}

==Rotate, Zoom, Pan==

{| border="1" width="100%" valign="top" cellspacing="3" cellpadding="3"
|style="background:#ffefd5;"|'''Interface Device/Action'''
|style="background:lightyellow;" |'''Rotate''' (3D viewers only)
|style="background:lightyellow;" |'''Zoom'''
|style="background:lightyellow;" |'''Pan'''
|-
|style="background:bisque;" |'''3-button'''
|Left-click & drag
|Right-Click & vertical drag
|Middle-Click & drag
|-
|style="background:bisque;" |'''2-button'''
|Left-click & drag
|Right-Click & vertical drag
|Shift+Left-Click & drag
|-
|style="background:bisque;" |'''1-button'''
|Left-click & drag
|Ctrl+Left-Click & vertical drag
|Shift+Left-Click & drag
|-
|style="background:bisque;" |'''1-button Mac'''
|Left-click & drag
|[[image:Apple-Command.png]](command)+Left-Click & vertical drag
|Shift+Left-Click & drag
|-
|style="background:bisque;" |'''Trackpad Mac'''
|Left-click & drag
|two-fingers & vertical drag
|Shift+Left-Click & drag
|}

==Selecting & Manipulating==
Mousing over any "pickable" object in any of Slicer's viewers will cause the cursor to change from a "pointer" into a "picking hand". When the cursor shows a picking hand, left-clicking and dragging the mouse will pick and manipulate the object. Releasing the mouse button will de-select the object.

==Mouse Modes==
{|
|-
|Slicer has two mouse modes: Transform, and Place. The icons in the mouse mode toolbar at the top of the main GUI allow to switch between these mouse modes and to modulate their behavior.

*'''Transform mode''' is the '''default''' interaction mode. This mode allows interactive rotation (3D viewer only), pan/translation and zoom (see above).
*'''Place''' mode allows to place one object then switches modes back to '''Transform''' mode. Place mode can be made persistent by clicking the checkbox adjacent to place mode. This allows to place multiple objects (e.g. fiducials).
**Fiducial is the default object in Place mode
**Ruler and Region Of Interest (ROI) Widgets are other available objects in the Place Mode menu.
|[[image:MouseModeToolbar-2011-12.png|thumb|200px|Mouse Mode Toolbar Transform icon to the left]]
|}

=Keyboard Accelerators=
*On Mac OS X use the Command key ([[image:Apple-Command.png]]) instead of the Control (Ctrl) key
*fn-Delete is used for Forward Delete on built-in keyboards of portable Macs

''Note that in addition to the global keyboard accelerators listed here, individual modules may define their own accelerators that are active when the module is active. See the [[Documentation/{{documentation/version}}/Modules/Editor#Keystrokes|Editor keyboard shortcuts]] for example.

==General==

{| class="wikitable"
|- border="1"
! align="left" |Key
! align="left" |Effect
|-
| style="width:200px" | '''Ctrl+O'''
| align="left"|Load a new scene (clears existing scene)
|-
| style="width:200px"|'''Ctrl+A'''
| align="left"|Import a scene (does not clear existing scene) Brings up '''Add Data''' instead
|-
| style="width:200px" |'''Ctrl+S'''
| align="left"| Save a scene
|-
| style="width:200px" |'''Ctrl+W'''
| align="left"| Close a scene
|-
| style="width:200px" |'''Ctrl+Z'''
| align="left"| Undo the history of undoable commands, from last to first.
|-
| style="width:200px" |'''Ctrl+Y'''
| align="left"| Redo the history of undoable commands, from last to first.
|-
| style="width:200px" |'''Ctrl+H'''
| align="left"| Set current module to "home" module for easy access.
|-
| style="width:200px"| '''Space'''
| align="left"| Toggles the display of Slicer's Edit Box.
|-
| style="width:200px" | '''Ctrl+P '''
| align="left"| Display the Python console '''Displays the QT-real console'''
|-
| style="width:200px" | '''Ctrl+L '''
| align="left" | Create a new fiducial list.
|-
| style="width:200px" | '''Ctrl+I'''
| align="left" | Toggle between "Persistent Place" and "Transform View" interaction modes.
|-
| style="width:200px" | '''Ctrl+M '''
| align="left" | Create a new Ruler measurement between the last two placed fiducials.
|-
| style="width:200px" | '''Ctrl+0 '''
| align="left" | Display error log.
|-
| style="width:200px" | '''Ctrl+1 '''
| align="left" | Interface documentation.
|-
| style="width:200px" | '''Ctrl+2 '''
| align="left" | Display the '''Application Settings Interface''' for customizing Slicer.
|-
| style="width:200px" | '''Ctrl+3 '''
| align="left" | Python Interactor.
|-
| style="width:200px" | '''Ctrl+4 '''
| align="left" | Extension Manager.
|-
| style="width:200px" | '''Ctrl+5 '''
| align="left" | Toggle Module Panel visible/invisible.
|-
| style="width:200px" | '''Ctrl+F '''
| align="left" | Select module search box
|-
| style="width:200px" | '''Ctrl+Left '''
| align="left" | Go to previous module in history.
|-
| style="width:200px" | '''Ctrl+Right '''
| align="left" | Go to next module in history.
|}

== 3D Viewer==

{| class="wikitable"
|- border="1"
! align="left" |Key
! align="left" |Effect
|- style="width:200px" | 
|'''r'''
| align="left"| Fits the cameras field of view to show all that is visible in the viewer
|-
| style="width:200px" |'''w '''
| align="left" | Show triangulated surface models as wireframe.
|-
| style="width:200px" |'''s '''
| align="left" | Show triangulated surface models as shaded surfaces.
|}

== Slice Viewer==

{| class="wikitable"
|- border="1"
! align="left" |Key
! align="left" |Effect
|-
| style="width:200px" | '''v'''
| align="left"| Toggles the slice plane visibility in the main 3D Viewer
|-
| style="width:200px" | '''r'''
| align="left""| Fits the slice view to the volume extents in the active Slice Viewer, or in all viewers if they are linked (the first non-none volume will be used in order of Background, Foreground and Label layers)
|-
| style="width:200px" | '''g'''
| align="left""| Toggles the opacity of the label layer
|-
| style="width:200px" | '''t'''
| align="left""| Toggles the opacity of the foreground layer
|-
| style="width:200px" | '''b''' or '''f'''
| align="left"| Decrease or increase visible slice in the active Slice Viewer (left or down) by one unit of background pixel spacing
|-
| style="width:200px" | '''[''' or ''']'''
| align="left"| Change background volume by cycle forward or backward through the volumes loaded in the scene
|-
| style="width:200px" | '''{''' or '''}'''
| align="left"| Change foreground volume by cycle forward or backward through the volumes loaded in the scene
|-
| style="width:200px" | '''` (back-tick)'''
| align="left" |Navigate to next fiducial in the active Slice Viewer, or in all viewers if they are linked (back-tick is the left single-quote on the key with the tilde (~) character in the upper left side of the keyboard) ''Reserved, but not yet implemented in Slicer 4.x''
|-
| style="width:200px" | '''Ctrl+` (back-tick)'''
| align="left" |Navigate to next fiducial in all Slice Viewers, independent of their linked state ''Reserved, but not yet implemented in Slicer 4.x''
|-
| style="width:200px" | '''Shift+` (back-tick)'''
| align="left" | Navigate to the previous fiducial in the active Slice Viewer, or in all viewers if they are linked ''Reserved, but not yet implemented in Slicer 4.x''
|-
| style="width:200px" | '''Ctrl+Shift+` (back-tick)'''
| align="left" | Navigate to the previous fiducial in all Slice Viewers, independent of their linked state ''Reserved, but not yet implemented in Slicer 4.x''
|-
| style="width:200px" | '''p'''
| align="left" | Place a new fiducial in the active Slice Viewer(adds to the current fiducial list, or creates a list if there are none) ''Reserved, but not yet implemented in Slicer 4.x''
|-
| style="width:200px" | '''Backspace'''
| align="left" | When the mouse is hovering over a fiducial in the Slice Viewer (turning it yellow), delete that fiducial ''Reserved, but not yet implemented in Slicer 4.x''
|-
| style="width:200px" | (forward)'''Delete'''
| align="left" | When the mouse is hovering over a fiducial in the Slice Viewer (turning it yellow), delete that fiducial ''Reserved, but not yet implemented in Slicer 4.x''
|-
| style="width:200px" | '''s'''
| align="left" | Selects the active slice in lightbox mode ''Reserved, but not yet implemented in Slicer 4.x''
|}

==Transfer Functions==
[[image:VolumeRendering-TransferFunction.png|thumb|right|348px|Transfer function in Volume Rendering module]]

* Current point (larger radius point)
** '''Left click''' on an existing point : make a point current
** '''Right arrow key''' or '''Top arrow key''': Make next point current
** '''Left arrow key''' or '''Bottom arrow key''': Make previous point current
** '''Left click & drag''': Move current point
** '''Ctrl & arrow key''': Move current point horizontally & vertically'' ''(to do)''
* Add a point
** '''Left click''' in an empty space
* Remove a point
** '''Middle click''': Remove and make next point current
** '''Backspace key''': Remove and make previous point current
** '''Del[ete] key''': Remove and make next point current
* Multi-selection (blue points)
** '''Right click & drag''': Select points inside rubber band area
** '''Right click''' a point: Toggle point selection
** '''Space key''': Toggle current point
** '''Shift & arrow key''': Select next/previous point
** '''Left click & drag''': Move selected points
** '''Ctrl & arrow key''': Move selected points'' ''(to do)''
** '''+ key''': Expand selected points
** '''- key''': Contract selected points
* Zoom
** '''Mouse wheel''' zooms in and out the view

=Non-Slicer Keybindings for Win, Mac, and Ubuntu=
*This section was inserted for compatibility considerations.

*source: http://www.pcmag.com/article2/0,2817,2400112,00.asp
==Keyboard Shortcuts—Windows==

Note: Single letter keys are shown capitalized, but you do not have to hold Shift unless it's specified. You also don't have to type the plus sign; plus sign just means push the keys on either side of it at the same time.

*Commonly Used OS-Level Shortcuts
#. Alt + Tab (toggle between programs)
#. Windows button + M (show desktop, i.e., minimize all windows)
#. Windows button + Tab (show all active windows in task bar)
#. PrtScn (save screen capture to clipboard; "paste" the image into an image-editing program to make it into a file)
#. Windows button (opens applications menu)

*Browser Shortcuts
#. Ctrl + T (open a new tab)
#. Ctrl + Shift + t (reopens the tab you last closed; works multiple times)
#. F5 (reload page)
#. Backspace (go to previous page; works multiple times)
#. Ctrl + Tab (cycle between tabs)

*Commonly Used Shortcuts in Most Applications
#. Ctrl+ Z (undo last operation)
#. Ctrl + Y (redo last operation)
#. Crtl + O (open file)
#. Crtl + S (save)
#. Ctrl + W (close active window or file)
#. Crtl + Q (quit application)

*Copy-and-Pasters' Delight
#. Ctrl + A (select all in active window; e.g., select all text on page)
#. Ctrl + X (cut to clipboard)
#. Ctrl + C (copy)
#. Ctrl + V (paste)

*Find, Select, and Navigate Text
#. Ctrl + F (find; helpful if you're searching for a particular word on a website or document)
#. Ctrl + Shift + down arrow (select until end of line)
#. Ctrl + Shift + up arrow (select until beginning of line)
#. Ctrl + Home (move cursor to top/start of document)
#. Ctrl + End (move cursor to bottom/end of document)

==Keyboard Shortcuts—Mac==

Note: Single letter keys are shown capitalized, but you do not have to hold Shift unless it's written. You also don't have to type the plus sign; plus sign just means push the keys on either side of it at the same time.

*Commonly Used OS-Level Shortcuts
#. Command + Tab (toggle between programs)
#. Command + M (minimize active window)
#. Swipe three fingers up on trackpad (show all active windows)
#. Command + Shift + 3 (take screen shot; the default settings will save it to a predefined location, usually the "Pictures" folder and name it "Picture1," "Picture2," etc.)
#. Command + N (opens new Finder from desktop; new window/file in most other programs)

*Browser Shortcuts
#. Command + T (open a new tab)
#. Command + Shift + t (reopens the tab you last closed in Chrome, Firefox, Opera; works multiple times)
#. Command + R (reload page)
#. Backspace (go to previous page; works multiple times)
#. Control + Tab (cycle between tabs/go to next tab in Chrome, Firefox, Opera)

*Commonly Used Shortcuts in Most Applications
#. Command + Z (undo last operation)
#. Command + Y (redo last operation)
#. Command + O (open file)
#. Command + S (save)
#. Command + W (close active window or file)
#. Command + Q (quit application)

*Copy-and-Pasters' Delight
#. Command + A (select all in active window; e.g., select all text on page)
#. Command + X (cut to clipboard)
#. Command + C (copy)
#. Command + V (paste)

*Find, Select, and Navigate Text
#. Command + F (find; helpful if you're searching for a particular word on a website or document)
#. Command + Shift + down arrow (select until end of line)
#. Command + Shift + up arrow (select until beginning of line)
#. Command + up arrow (move cursor to top/start of document)
#. Command + down arrow (move cursor to bottom/end of document)

==Keyboard Shortcuts-Ubuntu==
[https://help.ubuntu.com/community/KeyboardShortcuts Ubuntu Keyboard Shortcuts] are listed on this webpage.

== Python Interactor ==
* '''Ctrl + H''' : Print help message
* '''Ctrl + R''' : Open a file dialog to select a file to run

Documentation/4.10/SlicerApplication/LookupTables/TractographyColors

2018-10-19T00:48:17Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/TractographyColors}}


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This LUT is Work in Progress, which means:
* the label integers and values may change at any time
}}

*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
* If changing the order of the table, the indices can be recreated with [[Slicer3:LUTs_and_Ontologies:Renumber_Script|this tcl script]].

This is the look-up table for the parcellation of the white matter of the brain.
*Authors: Ron Kikinis, Demian Wassermann, Marianna Jakab

==Lookup table==

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
|0
|
|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
|background
|-
|1
|corpus callosum
|style="background:rgb(255, 215, 0)"|rgb(255, 215, 0)
|CC
|-
|2
|genu of the corpus callosum
|style="background:rgb(225, 215, 0)"|rgb(225, 215, 0)
|CC genu
|-
|3
|body of the corpus callosum
|style="background:rgb(195, 215, 0)"|rgb(195, 215, 0)
|CC body
|-
|4
|splenium of the corpus callosum
|style="background:rgb(165, 215, 0)"|rgb(165, 215, 0)
|CC splenium
|-
|5
|dorsal hippocampal comissure
|style="background:rgb(122, 150, 170)"|rgb(122, 120, 170)
|DHC
|-
|6
|anterior comissure
|style="background:rgb(92, 140, 170)"|rgb(92, 140, 170)
|AC
|-
|7
|posterior comissure
|style="background:rgb(62, 160, 170)"|rgb(62, 160, 170)
|PC
|-
|8
|forniceal comissure
|style="background:rgb( 32, 180, 170)"|rgb( 32, 180, 170)
|FC
|-
|9
|pontine tract
|style="background:rgb(92, 161, 124)"|rgb(92, 161, 124)
|PT
|-
|10
|short cortico-cortical pathway
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|U
|-
|11
|right arcuate fasicle
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|r AF
|-
|12
|left arcuate fasicle
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|l AF
|-
|13
|right inferior occipito-frontal fasicle
|style="background:rgb(144,238,144)"|rgb(144,238,144)
|r IOFF
|-
|14
|left inferior occipito-frontal fasicle
|style="background:rgb( 60, 179, 113)"|rgb( 60, 179, 113)
|l IOFF
|-
|15
|right inferior longitudinal fasicle
|style="background:rgb(220,245,20)"|rgb(220,245,20)
|r ILF
|-
|16
|left inferior longitudinal fasicle
|style="background:rgb(176, 176, 8)"|rgb(176, 176, 8)
|l ILF
|-
|17
|right uncinate fasicle
|style="background:rgb(255,250,220)"|rgb(255,250,220)
|r UF
|-
|18
|left uncinate fasicle
|style="background:rgb(230,220,70)"|rgb(230,220,70)
|l UF
|-
|19
|right cortico-spinal tract
|style="background:rgb(230, 230, 250)"|rgb(230, 230, 250)
|r CST
|-
|20
|left cortico-spinal tract
|style="background:rgb(200,200,235)"|rgb(200,200,235)
|l CST
|-
|21
|right optic radiation
|style="background:rgb(135, 206, 235)"|rgb(135, 206, 235)
|r OR
|-
|22
|left optic radiation
|style="background:rgb(0,151,206)"|rgb(0,151,206)
|l OR
|-
|23
|right cingulum bundle
|style="background:rgb(255, 99, 71)"|rgb(255, 99, 71)
|r CB
|-
|24
|left cingulum bundle
|style="background:rgb(250, 90, 90)"|rgb(250, 90, 90)
|l CB
|-
|25
|right superior longitudinal fasicle I
|style="background:rgb(183,214,211)"|rgb(183,214,211)
|r SLF I
|-
|26
|left superior longitudinal fasicle I
|style="background:rgb(152,189,207)"|rgb(152,189,207)
|l SLF I
|-
|27
|right superior longitudinal fasicle II
|style="background:rgb(178,212,242)"|rgb(178,212,242)
|r SLF II
|-
|28
|left superior longitudinal fasicle II
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|l SLF II
|-
|29
|right superior longitudinal fasicle III
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|r SLF III
|-
|30
|left superior longitudinal fasicle III
|style="background:rgb(68,172,100)"|rgb(68,172,100)
|l SLF III
|-
|31
|right middle longitudinal fasicle
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|r MdLF
|-
|32
|left middle longitudinal fasicle
|style="background:rgb( 65, 105, 225)"|rgb( 65, 105, 225)
|l MdLF
|-
|33
|right extreme capsule
|style="background:rgb(196, 110, 0)"|rgb(196, 110, 0)
|r EmC
|-
|34
|left extreme capsule
|style="background:rgb(176, 90, 50)"|rgb(160, 82, 45)
|l EmC
|-
|35
|right superior occipito-frontal fasicle
|style="background:rgb(216,191,216)"|rgb(216,191,216)
|r SOFF
|-
|36
|left superior occipito-frontal fasicle
|style="background:rgb(221, 160, 221)"|rgb(221, 160, 221)
|l SOFF
|-
|37
|right cortico-thalamical pathways
|style="background:rgb(245, 222, 179)"|rgb(245, 222, 179)
|r CT
|-
|38
|left cortico-thalamical pathways
|style="background:rgb(210, 180, 140)"|rgb(210, 180, 140)
|l CT
|-
|39
|right cortico-striatal pathways
|style="background:rgb(244, 164, 96)"|rgb(244, 164, 96)
|r CS
|-
|40
|left cortico-striatal pathways
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|l CS
|-
|41
|right cortico-pontine projections
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|r CP
|-
|42
|left cortico-pontine projections
|style="background:rgb(200,200,200)"|rgb(200,200,200)
|l CP
|-
|43
|peritumoral fibers
|style="background:rgb(100, 177, 198)"|rgb(100, 177, 198)
|PF
|-
|44
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|45
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|46
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|47
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|48
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|49
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|50
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|51
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|52
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|53
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|54
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|55
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|56
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|57
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|58
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|59
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|60
|
|style="background:rgb(255,255,255)"|rgb(255,255,255)
|
|-
|61
|Probe 1
|style="background:rgb(252,115,105)"|rgb(252,115,105)
|P1
|-
|62
|Probe 2
|style="background:rgb(222,115,105)"|rgb(222,115,105)
|P2
|-
|63
|Probe 3
|style="background:rgb(192,115,105)"|rgb(192,115,105)
|P3
|-
|64
|Probe 4
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|P4
|}

Documentation/4.10/SlicerApplication/MainApplicationGUI

2018-10-19T00:48:17Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/slicerapplication-header}}


=Overview=
{|width="100%"
|
__TOC__

|align="right"|
[[image:Slicer4ApplicationGUIMap.jpg|450px|Slicer Main GUI]]
|}
Slicer4'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.

==Application Menu==

Slicer's Application Menu contains many useful features. A brief overview of some of these is given below.

*File Menu
**The File Menu contains options for loading a [[Documentation/{{documentation/version}}/MRML|MRML]] scene, for downloading sample datasets from the internet, or individual datasets of various types. An option for saving scenes and data is also provided here.
*Edit Menu
**The Edit menu contains an option to raise the [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings|Application Settings Interface]]. This interface allows users to customize their installation of Slicer. '''Edit->Application Settings'' can be used to include or suppress various Slicer modules, to customize the appearance of your Python Interactor, to select a custom font, to specify a temporary directory, and to accomplish other customizations as well.
*View Menu
**This menu contains options to raise the Python Interactor and the [[Documentation/{{documentation/version}}/SlicerApplication/ErrorLog|Error Log]], both useful developer tools. Menu options to switch layouts, and to toggle the display of individual toolbars and the module GUI panels are also provided under the View Menu.

[[image: Slicer4AppMenu.jpg | center]]

==Toolbar==

The Toolbar provides shortcuts to many useful sets of functionality. The following toolbars appear here by default. Customization is possible from the Slicer View Menu.

===Load & Save Options===
The '''Load Scene''' option will raise a browser to select and load a collection of data as a MRML scene. This option clears the existing scene and resets the application state. The '''Save''' option will raise the "Save Data" Interface which offers a variety of options for saving MRML scenes and individual datasets.
===Module Selection & Navigation===
The Module Selection & Navigation toolbar provides options for searching for module names, selecting from a module menu, and moving backward and forward through the module selection history for convenience.

Clicking on the search icon and starting to type will display and update a list of module starting with the same letters.

Additional modules can be installed using the [[Documentation/{{documentation/version}}/SlicerApplication/ExtensionsManager|Extensions Manager]] or by updating the [[Documentation/Nightly/SlicerApplication/ApplicationSettings#Additional_module_paths|Additional Module Paths]] application settings.

===Core Modules (aka Favorites)===
The Core Module Toolbar provides shortcuts to your "Home" module, and some of Slicer's core modules including
* Models
* Transforms
* Data
* Volumes
* Annotations
* Interactive Editor

The list can be configured updating the [[Documentation/{{documentation/version }}/SlicerApplication/ApplicationSettings#Favorites|Favorites]] application settings.

===Layouts===
The Layout Toolbar provides a drop-down menu of layouts useful for many types of studies. When Slicer is exited normally, the selected layout is saved and restored as part of the Application state.
[[image:Slicer4Layouts.jpg | center]]

{{:Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI/MouseModes}}

===Screenshots & Scene Views===
[[image:Slicer4CaptureToolbar.png | center]]
This toolbar presents options for capturing screenshots (1st icon) and '''Scene Views''' (2nd icon) and restoring saved scene views (3rd icon).
*A '''Screenshot''' can be taken at multiples of the resolution visible on the screen. This allows the taking of higher quality pictures for publication. Saving the screenshots is possible in the save menu. At that time the format of the file can be specified. More information on saving is in the [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Load_.26_Save_Options|Load and Save toolbar]].
*A '''Scene View''' is a description of the state of the MRML scene at the time of its capture that can be restored at any time. This mechanism is useful for preparing and viewing multiple interesting presentations of a complicated dataset. More information in the [[Documentation/{{documentation/version}}/Modules/SceneViews|Scene Views module]].

===Crosshair Options===
The Crosshair Toolbar provides a set of options for customizing the appearance and behavior of the crosshairs across all Slice Viewers.
[[ image:Slicer4CrosshairOptions.jpg | center]]

See also [[#Viewer_Cross-Reference_on_All_Platforms|Viewer Cross-Reference on All Platforms]]

==Module Panel==

Any selected module in Slicer will display its user interface in the '''Module Panel'''. The panel may be undocked (by left-clicking & dragging the panel's title bar or by clicking its undock icon; hidden by selecting the hide (X) icon, or have its display toggled by selecting View->Module Panel. The panel can be re-docked by double-clicking on its title bar or frame.

==Data Probe==

The Data Probe interactively reports data values at voxels indexed by the current mouse position in all layers (Label, Foreground and Background).

See the [[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe documentation]] for more information about the data values displayed.

== 3D Viewer ==

Access the 3D Viewer Controller by mousing over the '''push-pin''' icon in the top left corner of any 3D Viewer.
*The panel may be opened persistently by clicking the '''push-pin''' icon which effectively "pins" it open. Clicking again "unpins" the panel.
*Next to the push-pin, a '''unique ID''' may be found that distinguishes this 3D viewer from other 3D viewers that may have been created when other layouts were selected.
*Finally there is a '''Center the View''' button to set the virtual camera to show everything that is visible in the viewer at that point.
*The '''panel''' contains options for setting the viewpoint direction, and configuring the appearance and behavior of any 3D Viewer. This includes buttons to set slicer to rock or orbit in the irghtmost column. The eye icon contains controls for visibility of the orientation letters and the bounding box in the 3D viewer.
* Depth peeling is a multipass technique to render translucent polygonal geometry without sorting polygons. It can be used to solve semi-transparent surface model rendering issues.
[[image:Slicer43DViewController.png | 602px| center ]]

== Slice Viewers ==

Each Slice Viewer supports three '''layers''': (Foreground or '''FG''', Background or '''BG''', and Label or '''L''') that can be viewed separately, or blended together in a customizable fashion. When a new scalar volume is loaded, it is automatically displayed in the BG layer. When a new label map is loaded, it is automatically loaded into the L layer. The contents of these layers can be selectively changed in any Slice Viewer's control panel.

Access any Slice Viewer's Controller by mousing over its '''push-pin''' icon in the top left corner of any slice viewer. The panel may also be opened persistently by clicking the push-pin icon. Next to the push-pin a unique ID may be found that distinguishes the particular Slice Viewer from other Slice Viewers that may have been created when other layouts were selected. A '''Slice Scrollbar''' is provided for manually sweeping through slices and a slice number entry widget is also provided at the top right of the display for manually indexing a particular slice. Each Slice Viewer contains options for displaying each of the layers (Foreground, Background and Label). For the Foreground and Label layers, the opacity of the layer can be controlled by using the spinbox opacity widget (pointed by the "Opacity" annotation in the figure below). In addition, the visibility of the Label layer can be toggled between the "contour" and "solid" mode (see "Label contour" button in the diagram below).

Some Slice Viewer configuration options may be applied to '''one or all''' Slice Viewers by using the '''Link''' option. When viewers are unlinked, an option applies only to the viewer being adjusted. When viewers are linked, the option will apply to '''all''' Slice Viewers. The application of an operation or interaction when viewers are linked is propagated to the other viewers only after the interaction with the current viewer is complete. For example, zooming within a viewer when the viewers are linked will interactively zoom the current viewer and upon completion of the interaction, the effect of the zoom will be propagated to the other viewers. The '''Hot-Link''' setting modifies this behavior such the effect of an interaction is immediately applied to all viewers. Link and Unlink are persistent settings. The linking behavior for Slice Viewer settings and interactions is further describe [[Slicer3:UIDesign:WorkingProblems:LinkedControls | here]].

[[image:SliceViewerController-4.1.png | center]]

== Chart Viewers ==

Access any Chart Viewer's Controller by mousing over its '''push-pin''' icon in the top left corner of any chart viewer. The panel may also be opened persistently by clicking the push-pin icon. Next to the push-pin a unique ID may be found that distinguishes the particular Chart Viewer from other Chart Viewers that may have been created when other layouts were selected. Each Chart Viewer contains options for controlling the content and display of a Chart.

The content and display of a Chart is controlled by selecting a specific Chart for the Chart Viewer. A Chart Viewer can switch between multiple Charts by selecting different Charts from the Scene. The type of the chart can '''Line''', '''Bar''', or '''Scatter'''. The style can be modified by toggling the display of '''Lines''' and '''Markers''' for the data or by toggling the display of a '''Grid''' or the '''Legend'''. The content of the Chart can be modified by adding and removing individual '''Arrays''' from the Chart. The Chart's '''Title''', '''X-axis Label''', and '''Y-axis Label''' can be edited using the controls in the Chart Viewer's Controller.

== Mouse & Keyboard Across Platforms ==

Below is basic information about how to use the three-, two-, and one-button mouse (or trackpad) on
Windows, Mac, and Linux platforms to perform basic interaction operations in Slicer.

===Adjusting Window & Level on All Platforms===

Left-clicking and dragging the mouse in any Slice viewer is a quick way to adjust Window and Level. Adjust the middle value (level) of the greyscale window by moving the mouse up (increase level) or down (decrease level), and adjust the greyscale window size by moving the mouse to the left (decrease window size) or right (increase window size). Slicer's '''Volumes Module''' provides a "Display" interface panel for making more precise adjustments.

===Selecting & Manipulating on All Platforms ===

Mousing over any "pickable" object in any of Slicer's viewers will cause the cursor to change from a "pointer"
into a "picking hand". When the cursor shows a picking hand, left-clicking and dragging the mouse will pick and
manipulate the object. Releasing the mouse button will deselect the object.

===Viewer Cross-Reference on All Platforms ===

Holding down the '''Shift-Key''' while moving the mouse in any Slice Viewer will cause other
Slice Viewers to interactively scroll to the same RAS position indexed by the mouse. This feature
is useful when inspecting multiple registered studies.

===Zoom In & Out in Slice & 3D Viewers ===

* '''Windows, Mac & Linux''' with
** '''3-Button Mouse:''' Right-click & drag down & up
** '''2-Button Mouse:''' Right-click & drag down & up
** '''1-Button Mouse:''' Ctrl+Left-click & drag down & up
* '''Mac with trackpad''': two-finger click & drag

===Pan (Translate) in Slicer & 3D Viewers ===

* '''Windows, Mac & Linux''' with
** '''3-Button Mouse:''' Middle-click & drag
** '''2-Button Mouse:''' Shift+Left-click & drag
** '''1-Button Mouse:''' Shift+Left-click & drag

===Rotate in 3D Viewers ===

* '''Windows, Mac & Linux''' with
** '''3-Button Mouse:''' Left-click & drag
** '''2-Button Mouse:''' Left-click & drag
** '''1-Button Mouse:''' Left-click & drag

{{:Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI/MouseModes}}

{{:Documentation/{{documentation/version}}/FAQ/UserInterface|User Interface}}


{{documentation/{{documentation/version}}/slicerapplication-footer}}

Documentation/4.10/SlicerApplication/LookupTables/Mori-Atlas labels

2018-10-19T00:48:16Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
[[Slicer3:LUTs_and_Ontologies|Back to LUTs and Ontologies]]

*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format. '''WARNING''': the conversion fails on the alpha channel if using rgba(R, G, B, 255) instead of rgb(R, G, B) or rgba(R, G, B, 1.0). If the last column of the generated text file contains 65025, change it to 255.
* [[Slicer3:Mori-Atlas_labels_JHU-MNI_SS_Type-I]]
* [[Slicer3:Mori_Atlas_labels_JHU-MNI_SS_Type-II]]
* [[Slicer3:Mori_Atlas_labels_JHU-MNI_SS_Type-III]]
*List

=Look-up Table for the Mori WM Atlas labels=
Work in progress.
{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
|-
| 0
| Background
|style="color:white; background:black"| rgba(0,0,0,0)
|-
| 1
| MCP_Middle_cerebellar_peduncle
| style="background:gold"| gold
|-
| 2
| PCT_Pontine_crossing_tract_(a_part_of_MCP) genotype
| style="background:navajowhite"| navajowhite
|-
| 3
| GCC_Genu_of_corpus_callosum
| style="background:plum"| plum
|-
| 4
| BCC_Body_of_corpus_callosum
| style="background:pink"| pink
|-
| 5
| SCC_Splenium_of_corpus_callosum
| style="background:deeppink"| deeppink
|-
|6
| FX_Fornix_(column_and_body_of_fornix)
| style="background:peru"| peru
|-
|7
| CST-R_Corticospinal_tract_right
| style="background:tan"| tan
|-
| 8
| CST-L_Corticospinal_tract_left
| style="background:tan"| tan
|-
| 9
| ML-R_Medial_lemniscus_right
| style="background:mediumspringgreen"| mediumspringgreen
|-
| 10
| ML-L_Medial_lemniscus_left
| style="background:mediumspringgreen"| mediumspringgreen
|-
| 11
| ICP-R_Inferior_cerebellar_peduncle_right
| style="background:palegreen"| palegreen
|-
| 12
| ICP-L_Inferior_cerebellar_peduncle_left
| style="background:palegreen"| palegreen
|-
| 13
| SCP-R_Superior_cerebellar_peduncle_right
| style="background:bisque"| bisque
|-
| 14
| SCP-L_Superior_cerebellar_peduncle_left
| style="background:bisque"| bisque
|-
| 15
| CP-R_Cerebral_peduncle_right
| style="background:khaki"| khaki
|-
| 16
| CP-L_Cerebral_peduncle_left
| style="background:khaki"| khaki
|-
| 17
| ALIC-R_Anterior_limb_of_internal_capsule_right
| style="background:lightskyblue"| lightskyblue
|-
| 18
| ALIC-L_Anterior_limb_of_internal_capsule_left
| style="background:lightskyblue"| lightskyblue
|-
| 19
| PLIC-R_Posterior_limb_of_internal_capsule_right
| style="background:dodgerblue"| dodgerblue
|-
| 20
| PLIC-L_Posterior_limb_of_internal_capsule_left
| style="background:dodgerblue"| dodgerblue
|-
| 21
| RLIC-R_Retrolenticular_part_of_internal_capsule_right
| style="background:deepskyblue"| deepskyblue
|-
| 22
| RLIC-L_Retrolenticular_part_of_internal_capsule_left
| style="background:deepskyblue"| deepskyblue
|-
| 23
| ACR-R_Anterior_corona_radiata_right
| style="background:powderblue"| powderblue
|-
| 24
| ACR-L_Anterior_corona_radiata_left
| style="background:powderblue"| powderblue
|-
| 25
| SCR-R_Superior_corona_radiata_right
| style="background:blue"| blue
|-
| 26
| SCR-L_Superior_corona_radiata_left
| style="background:blue"| blue
|-
| 27
| PCR-R_Posterior_corona_radiata_right
| style="background:skyblue"| skyblue
|-
| 28
| PCR-L_Posterior_corona_radiata_left
| style="background:skyblue"| skyblue
|-
| 29
| PTR-R_Posterior_thalamic_radiation_(include_optic_radiation)_right
| style="background:sandybrown"| sandybrown
|-
| 30
| PTR-L_Posterior_thalamic_radiation_(include_optic_radiation)_left
| style="background:sandybrown"| sandybrown
|-
| 31
| SS-R_Sagittal_stratum_(include_inferior_longitidinal_fasciculus_and_inferior_fronto-occipital_fasciculus)_right
| style="background:peachpuff"| peachpuff
|-
| 32
| SS-L_Sagittal_stratum_(include_inferior_longitidinal_fasciculus_and_inferior_fronto-occipital_fasciculus)_left
| style="background:peachpuff"| peachpuff
|-
| 33
| EC-R_External_capsule_right
| style="background:darksalmon"| darksalmon
|-
| 34
| EC-L_External_capsule_left
| style="background:darksalmon"| darksalmon
|-
| 35
| CGC-R_Cingulum_(cingulate_gyrus)_right
| style="background:mediumseagreen"| mediumseagreen
|-
| 36
| CGC-L_Cingulum_(cingulate_gyrus)_left
| style="background:mediumseagreen"| mediumseagreen
|-
| 37
| CGH-R_Cingulum_(hippocampus)_right
| style="background:darkkhaki"| darkkhaki
|-
| 38
| CGH-L_Cingulum_(hippocampus)_left
| style="background:darkkhaki"| darkkhaki
|-
| 39
| FX-R_Fornix_Stria_terminalis_right
| style="background:darkgoldenrod"| darkgoldenrod
|-
| 40
| FX-L_Fornix_Stria_terminalis_left
| style="background:darkgoldenrod"| darkgoldenrod
|-
| 41
| SLF-R_Superior_longitudinal_fasciculus_right
| style="background:lightgray"| lightgray
|-
| 42
| SLF-L_Superior_longitudinal_fasciculus_left
| style="background:lightgray"| lightgray
|-
| 43
| SFO-R_Superior_fronto-occipital_fasciculus_right
| style="background:darkgrey"| darkgrey
|-
| 44
| SFO-R_Superior_fronto-occipital_fasciculus_left
| style="background:darkgrey"| darkgrey
|-
| 45
| IFO-R_Inferior_fronto-occipital_fasciculus_right
| style="background:gray"| gray
|-
| 46
| IFO-L_Inferior_fronto-occipital_fasciculus_left
| style="background:gray"| gray
|-
| 47
| UNC-R_Uncinate_fasciculus_right
| style="background:brown"| brown
|-
| 48
| UNC-L_Uncinate_fasciculus_left
| style="background:brown"| brown
|-
| 49
| TAP-R_Tapetum_right
| style="background:mistyrose"| mistyrose
|-
| 50
| TAP-L_Tapetum_left
| style="background:mistyrose"| mistyrose
|}

Documentation/4.10/SlicerApplication/LookupTables/PCampReview

2018-10-19T00:48:16Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
[[Slicer3:LUTs_and_Ontologies|Back to LUTs and Ontologies]]

* [http://labelpage.halle.us/ Go here] To create a text file in Slicer LUT format. '''WARNING''': the conversion fails on the alpha channel if using rgba(R, G, B, 255) instead of rgb(R, G, B) or rgba(R, G, B, 1.0). If the last column of the generated text file contains 65025, change it to 255.

=Look-up Table for PCampReview=
Version 1.0
 

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
|-
| 0
| Background
|style="color:white; background:black"| rgba(0,0,0,0)
|-
| 1
| Tumor-1 in PZ
| style="background:rgb(255,204,0)"| rgb(255,204,0)
|-
| 2
| Tumor-2 in PZ
| style="background:rgb(255,204,0)"| rgb(255,204,0)
|-
| 3
| Tumor-3 in PZ
| style="background:rgb(255,204,0)"| rgb(255,204,0)
|-
| 4
| Tumor-4 in PZ
| style="background:rgb(255,204,0)"| rgb(255,204,0)
|-
| 5
| Tumor-5 in PZ
| style="background:rgb(255,204,0)"| rgb(255,204,0)
|-
|6
| Tumor-1 in CG
| style="background:rgb(153, 102, 51)"| rgb(153, 102, 51)
|-
|7
| Tumor-2 in CG
| style="background:rgb(153, 102, 51)"| rgb(153, 102, 51)
|-
| 8
| Tumor-3 in CG
| style="background:rgb(153, 102, 51)"| rgb(153, 102, 51)
|-
| 9
| Tumor-4 in CG
| style="background:rgb(153, 102, 51)"| rgb(153, 102, 51)
|-
| 10
| Tumor-5 in CG
| style="background:rgb(153, 102, 51)"| rgb(153, 102, 51)
|-
| 11
| Tumor-1 in TZ
| style="background:rgb(255, 204, 102)"| rgb(255, 204, 102)
|-
| 12
| Tumor-2 in TZ
| style="background:rgb(255, 204, 102)"| rgb(255, 204, 102)
|-
| 13
| Tumor-3 in TZ
| style="background:rgb(255, 204, 102)"| rgb(255, 204, 102)
|-
| 14
| Tumor-4 in TZ
| style="background:rgb(255, 204, 102)"| rgb(255, 204, 102)
|-
| 15
| Tumor-5 in TZ
| style="background:rgb(255, 204, 102)"| rgb(255, 204, 102)
|-
| 16
| Normal-1 in PZ
| style="background:rgb(51,204,0)"| rgb(51,204,0)
|-
| 17
| Normal-2 in PZ
| style="background:rgb(51,204,0)"| rgb(51,204,0)
|-
| 18
| Normal-3 in PZ
| style="background:rgb(51,204,0)"| rgb(51,204,0)
|-
| 19
| Normal-4 in PZ
| style="background:rgb(51,204,0)"| rgb(51,204,0)
|-
| 20
| Normal-5 in PZ
| style="background:rgb(51,204,0)"| rgb(51,204,0)
|-
| 21
| Normal-1 in CG
| style="background:rgb(51,102,51)"| rgb(51,102,51)
|-
| 22
| Normal-2 in CG
| style="background:rgb(51,102,51)"| rgb(51,102,51)
|-
| 23
| Normal-3 in CG
| style="background:rgb(51,102,51)"| rgb(51,102,51)
|-
| 24
| Normal-4 in CG
| style="background:rgb(51,102,51)"| rgb(51,102,51)
|-
| 25
| Normal-5 in CG
| style="background:rgb(51,102,51)"| rgb(51,102,51)
|-
| 26
| Normal-1 in TZ
| style="background:rgb(153,255,102)"| rgb(153,255,102)
|-
| 27
| Normal-2 in TZ
| style="background:rgb(153,255,102)"| rgb(153,255,102)
|-
| 28
| Normal-3 in CG
| style="background:rgb(153,255,102)"| rgb(153,255,102)
|-
| 29
| Normal-4 in TZ
| style="background:rgb(153,255,102)"| rgb(153,255,102)
|-
| 30
| Normal-5 in TZ
| style="background:rgb(153,255,102)"| rgb(153,255,102)
|-
| 31
| Obturator Muscle
| style="background:rgb(153,102,255)"| rgb(153,102,255)
|-
| 32
| Left Femoral Artery
| style="background:rgb(204,0,51)"| rgb(204,0,51)
|-
| 33
| Right Femoral Artery
| style="background:rgb(204,0,51)"| rgb(204,0,51)
|}

=References=
* [https://github.com/fedorov/PCampReview PCampReview Github Repository]
* [http://colorschemedesigner.com/ Color Scheme Designer]

Documentation/4.10/SlicerApplication/LookupTables/HNLabels

2018-10-19T00:48:15Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
=== Head and Neck Muscles ===
{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! integer_label
! text_label
! color
! notes
|-
|int4001
|4001
|left_temporalis
|style="background:rgb(153,0,51)"|rgb(153,0,51)
|
|-
|int4002
|4002
|right_temporalis
|style="background:rgb(153,0,51)"|rgb(153,0,51)
|
|-
|int4003
|4003
|left_masseter
|style="background:rgb(133,0,51)"|rgb(133,0,51)
|
|-
|int4004
|4004
|right_masseter
|style="background:rgb(133,0,51)"|rgb(133,0,51)
|
|-
|int4005
|4005
|left_lateral_pterygoid
|style="background:rgb(110,0,51)"|rgb(110,0,51)
|
|-
|int4006
|4006
|right_lateral_pterygoid
|style="background:rgb(110,0,51)"|rgb(110,0,51)
|
|-
|int4007
|4007
|left_medial_pterygoid
|style="background:rgb(90,0,51)"|rgb(90,0,51)
|
|-
|int4008
|4008
|right_medial_pterygoid
|style="background:rgb(90,0,51)"|rgb(90,0,51)
|
|-
|int4011
|4011
|left_medial_rectus
|style="background:rgb(90,79,145)"|rgb(90,79,145)
|
|-
|int4012
|4012
|right_medial_rectus
|style="background:rgb(90,79,145)"|rgb(90,79,145)
|
|-
|int4013
|4013
|left_superior_rectus
|style="background:rgb(111,88,147)"|rgb(111,88,147)
|
|-
|int4014
|4014
|right_superior_rectus
|style="background:rgb(111,88,147)"|rgb(111,88,147)
|
|-
|int4015
|4015
|left_superior_oblique
|style="background:rgb(123,98,130)"|rgb(123,98,130)
|
|-
|int4016
|4016
|right_superior_oblique
|style="background:rgb(123,98,130)"|rgb(123,98,130)
|
|-
|int4017
|4017
|left_inferior_rectus
|style="background:rgb(135,108,144)"|rgb(135,108,144)
|
|-
|int4018
|4018
|right_inferior_rectus
|style="background:rgb(135,108,144)"|rgb(135,108,144)
|
|-
|int4019
|4019
|left_lateral_rectus
|style="background:rgb(150,120,160)"|rgb(150,120,160)
|
|-
|int4020
|4020
|right_lateral_rectus
|style="background:rgb(150,120,160)"|rgb(150,120,160)
|
|-
|int4021
|4021
|left_levator_palpebrae_superioris
|style="background:rgb(170,120,160)"|rgb(170,120,160)
|
|-
|int4022
|4022
|right_levator_palpebrae_superioris
|style="background:rgb(170,120,160)"|rgb(170,120,160)
|
|-
|int4027
|4027
|left_eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|int4028
|4028
|right_eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|int4030
|4030
|uvula
|style="background:rgb(180,75,20)"|rgb(180,75,20)
|
|-
|int4031
|4031
|left_tensor_veli_palatini
|style="background:rgb(165,85,25)"|rgb(165,85,25)
|
|-
|int4032
|4032
|right_tensor_veli_palatini
|style="background:rgb(165,85,25)"|rgb(165,85,25)
|
|-
|int4033
|4033
|left_palatoglossus
|style="background:rgb(210,85,25)"|rgb(210,85,25)
|
|-
|int4034
|4034
|right_palatoglossus
|style="background:rgb(210,85,25)"|rgb(210,85,25)
|
|-
|int4035
|4035
|left_levator_veli_palatini
|style="background:rgb(255,85,25)"|rgb(255,85,25)
|
|-
|int4036
|4036
|right_levator_veli_palatini
|style="background:rgb(255,85,25)"|rgb(255,85,25)
|
|-
|int4037
|4037
|left_palatopharyngeus
|style="background:rgb(198,85,25)"|rgb(198,85,25)
|
|-
|int4038
|4038
|right_palatopharyngeus
|style="background:rgb(198,85,25)"|rgb(198,85,25)
|
|-
|int4041
|4041
|left_zygomaticus_major
|style="background:rgb(200,125,125)"|rgb(200,125,125)
|
|-
|int4042
|4042
|right_zygomaticus_major
|style="background:rgb(200,125,125)"|rgb(200,125,125)
|
|-
|int4043
|4043
|left_nasalis
|style="background:rgb(220,125,125)"|rgb(220,125,125)
|
|-
|int4044
|4044
|right_nasalis
|style="background:rgb(220,125,125)"|rgb(220,125,125)
|
|-
|int4045
|4045
|left_levator_labii_superioris
|style="background:rgb(210,125,125)"|rgb(210,125,125)
|
|-
|int4046
|4046
|right_levator_labii_superioris
|style="background:rgb(210,125,125)"|rgb(210,125,125)
|
|-
|int4047
|4047
|left_buccinator
|style="background:rgb(190,125,125)"|rgb(190,125,125)
|
|-
|int4048
|4048
|right_buccinator
|style="background:rgb(190,125,125)"|rgb(190,125,125)
|
|-
|int4050
|4050
|tongue
|style="background:rgb(166,84,94)"|rgb(166,84,94)
|
|-
|int4051
|4051
|left_hyoglossus
|style="background:rgb(180,115,115)"|rgb(180,115,115)
|
|-
|int4052
|4052
|right_hyoglossus
|style="background:rgb(180,115,115)"|rgb(180,115,115)
|
|-
|int4060
|4060
|middle_constrictor
|style="background:rgb(150,70,70)"|rgb(150,70,70)
|
|-
|int4061
|4061
|left_stylopharyngeus
|style="background:rgb(180,70,70)"|rgb(180,70,70)
|
|-
|int4062
|4062
|right_stylopharyngeus
|style="background:rgb(180,70,70)"|rgb(180,70,70)
|
|-
|int4071
|4071
|left_rectus_capitis_posterior_minor
|style="background:rgb(145,80,100)"|rgb(145,80,100)
|
|-
|int4072
|4072
|right_rectus_capitis_posterior_minor
|style="background:rgb(145,80,100)"|rgb(145,80,100)
|
|-
|int4073
|4073
|left_longissimus_capitis
|style="background:rgb(255,80,100)"|rgb(255,80,100)
|
|-
|int4074
|4074
|right_longissimus_capitis
|style="background:rgb(255,80,100)"|rgb(255,80,100)
|
|-
|int4075
|4075
|left_semispinalis_capitis
|style="background:rgb(255,100,80)"|rgb(255,100,80)
|
|-
|int4076
|4076
|right_semispinalis_capitis
|style="background:rgb(255,100,80)"|rgb(255,100,80)
|
|-
|int4077
|4077
|left_longus_colli
|style="background:rgb(215,100,80)"|rgb(215,100,80)
|
|-
|int4078
|4078
|right_longus_colli
|style="background:rgb(215,100,80)"|rgb(215,100,80)
|
|-
|int4079
|4079
|left_superior_oblique_capitis
|style="background:rgb(200,80,100)"|rgb(200,80,100)
|
|-
|int4080
|4080
|right_superior_oblique_capitis
|style="background:rgb(200,80,100)"|rgb(200,80,100)
|
|-
|int4081
|4081
|left_stylohyoid
|style="background:rgb(175,80,100)"|rgb(175,80,100)
|
|-
|int4082
|4082
|right_stylohyoid
|style="background:rgb(175,80,100)"|rgb(175,80,100)
|
|-
|int4083
|4083
|left_anterior_rectus_capitis
|style="background:rgb(215,100,80)"|rgb(215,100,80)
|
|-
|int4084
|4084
|right_anterior_rectus_capitis
|style="background:rgb(215,100,80)"|rgb(215,100,80)
|
|-
|int4085
|4085
|left_trapezius
|style="background:rgb(155,80,100)"|rgb(155,80,100)
|
|-
|int4086
|4086
|right_trapezius
|style="background:rgb(155,80,100)"|rgb(155,80,100)
|
|-
|int4087
|4087
|left_longus_capitis
|style="background:rgb(210,80,100)"|rgb(210,80,100)
|
|-
|int4088
|4088
|right_longus_capitis
|style="background:rgb(210,80,100)"|rgb(210,80,100)
|
|-
|int4089
|4089
|left_sternocleidomastoid
|style="background:rgb(160,80,100)"|rgb(160,80,100)
|
|-
|int4090
|4090
|right_sternocleidomastoid
|style="background:rgb(160,80,100)"|rgb(160,80,100)
|
|-
|int4091
|4091
|left_middle_scalenus
|style="background:rgb(165,80,100)"|rgb(165,80,100)
|
|-
|int4092
|4092
|right_middle_scalenus
|style="background:rgb(165,80,100)"|rgb(165,80,100)
|
|-
|int4093
|4093
|left_digastric
|style="background:rgb(170,80,100)"|rgb(170,80,100)
|
|-
|int4094
|4094
|right_digastric
|style="background:rgb(170,80,100)"|rgb(170,80,100)
|
|-
|int4095
|4095
|left_splenius_capitis
|style="background:rgb(180,80,100)"|rgb(180,80,100)
|
|-
|int4096
|4096
|right_splenius_capitis
|style="background:rgb(180,80,100)"|rgb(180,80,100)
|
|-
|int4097
|4097
|left_inferior_oblique_capitis
|style="background:rgb(185,80,100)"|rgb(185,80,100)
|
|-
|int4098
|4098
|right_inferior_oblique_capitis
|style="background:rgb(185,80,100)"|rgb(185,80,100)
|
|-
|int4099
|4099
|left_rectus_capitis_posterior_major
|style="background:rgb(215,80,100)"|rgb(215,80,100)
|
|-
|int4100
|4100
|right_rectus_capitis_posterior_major
|style="background:rgb(215,80,100)"|rgb(215,80,100)
|
|-
|}

Documentation/4.10/SlicerApplication/LookupTables/KneeAtlasLabels

2018-10-19T00:48:15Z

UpdateBot: Nightly -> 4.10

<noinclude>{{documentation/versioncheck}}</noinclude>
*Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format. '''WARNING''': the conversion fails on the alpha channel if using rgba(R, G, B, 255) instead of rgb(R, G, B) or rgba(R, G, B, 1.0). If the last column of the generated text file contains 65025, change it to 255.

=Knee Atlas Lookup Table=

Link to actual File: [[File:KneeAtlasLabels.txt]]

{|class="wikitable sortable labelpage labelpagetable" border="1"
|-
!integer_label
!text_label
!color
|-
|0
|(none)
| style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0.000)
|-
|9
|infrapatellar fat body
| style="background:rgb(230,220,70);color:black"|rgb(230,220,70)
|-
|12
|vastus lateralis muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|13
|vastus medialis muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|15
|biceps femoris muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|16
|semimembranosus muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|17
|semitendinosus muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|18
|gracilis muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|19
|sartorius muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|20
|medial head gastrocnemius muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|21
|lateral head gastrocnemius muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|22
|popliteus muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|23
|soleus muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|24
|tibialis anterior muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|25
|extensor digitorum longus muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|26
|peroneus longus muscle
| style="background:rgb(206,111,93);color:black"|rgb(206,111,93)
|-
|31
|anterior cruciate ligament
| style="background:rgb(183,214,211);color:black"|rgb(183,214,211)
|-
|32
|posterior cruciate ligament
| style="background:rgb(183,214,211);color:black"|rgb(183,214,211)
|-
|33
|fibular collateral ligament
| style="background:rgb(183,214,211);color:black"|rgb(183,214,211)
|-
|34
|tibial collateral ligament
| style="background:rgb(183,214,211);color:black"|rgb(183,214,211)
|-
|35
|patellar ligament
| style="background:rgb(183,214,211);color:black"|rgb(183,214,211)
|-
|41
|adductor magnus tendon
| style="background:rgb(152,189,207);color:black"|rgb(152,189,207)
|-
|42
|biceps femoris tendon
| style="background:rgb(152,189,207);color:black"|rgb(152,189,207)
|-
|43
|iliotibial tract
| style="background:rgb(240,220,220);color:black"|rgb(240,220,220)
|-
|44
|popliteus tendon
| style="background:rgb(152,189,207);color:black"|rgb(152,189,207)
|-
|46
|soleus tendon
| style="background:rgb(152,189,207);color:black"|rgb(152,189,207)
|-
|47
|semitendinosus tendon
| style="background:rgb(152,189,207);color:black"|rgb(152,189,207)
|-
|48
|gracilis tendon
| style="background:rgb(152,189,207);color:black"|rgb(152,189,207)
|-
|61
|peroneus nerve
| style="background:rgb(224,194,0);color:black"|rgb(224,194,0)
|-
|62
|tibialis nerve
| style="background:rgb(224,194,0);color:black"|rgb(224,194,0)
|-
|63
|muscular branches tibialis nerve
| style="background:rgb(224,194,0);color:black"|rgb(224,194,0)
|-
|64
|medial sural cutaneous nerve
| style="background:rgb(224,194,0);color:black"|rgb(224,194,0)
|-
|71
|popliteal artery
| style="background:rgb(216,101,79);color:black"|rgb(216,101,79)
|-
|72
|popliteal vein
| style="background:rgb(0,151,206);color:white"|rgb(0,151,206)
|-
|73
|superior medial genicular artery
| style="background:rgb(216,101,79);color:black"|rgb(216,101,79)
|-
|74
|superior lateral genicular artery
| style="background:rgb(216,101,79);color:black"|rgb(216,101,79)
|-
|75
|middle genicular artery
| style="background:rgb(216,101,79);color:black"|rgb(216,101,79)
|-
|77
|great saphenous vein
| style="background:rgb(0,151,206);color:white"|rgb(0,151,206)
|-
|78
|small saphenous vein
| style="background:rgb(0,151,206);color:white"|rgb(0,151,206)
|-
|81
|lateral meniscus
| style="background:rgb(178,212,242);color:black"|rgb(178,212,242)
|-
|82
|medial meniscus
| style="background:rgb(178,212,242);color:black"|rgb(178,212,242)
|-
|83
|femoral cartilage
| style="background:rgb(111,184,210);color:black"|rgb(111,184,210)
|-
|84
|lateral tibial cartilage
| style="background:rgb(111,184,210);color:black"|rgb(111,184,210)
|-
|85
|medial tibial cartilage
| style="background:rgb(111,184,210);color:black"|rgb(111,184,210)
|-
|86
|patellar cartilage
| style="background:rgb(111,184,210);color:black"|rgb(111,184,210)
|-
|95
|femur
| style="background:rgb(241,214,145);color:black"|rgb(241,214,145)
|-
|96
|tibia
| style="background:rgb(241,214,145);color:black"|rgb(241,214,145)
|-
|97
|fibula
| style="background:rgb(241,214,145);color:black"|rgb(241,214,145)
|-
|98
|patella
| style="background:rgb(241,214,145);color:black"|rgb(241,214,145)
|}