Nicole at 19:09, 15 November 2013

2013-11-15T19:09:25Z

UpdateBot: Nightly -> 4.3

2013-09-05T03:33:49Z

Nightly -> 4.3

New page

<noinclude>{{documentation/versioncheck}}</noinclude>
__NOTOC__
=Overview=
Slicer offers a variety of predefined lookup tables (LUT). Volumes can be associated with a LUT in the volumes module. Also, see the [[Documentation/{{documentation/version}}/Modules/Colors|Colors Module]].

==LUTs==
<gallery widths=175px>
file:DiscreteLUTs-2012-02-18.png|''Discrete LUTs''
file:Shade-LUTs-2012-02-18.png|''Shade LUTs''
file:Tint-LUTs-2012-02-18.png|''Tint LUTs''
file:Freesurfer-LUTs-2012-02-18.png|''Freesurfer LUTs'' -[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]]
file:PET-LUTs-2012-02-18.png|''PET LUTs''
file:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
file:Labelmap-LUTs-2012-02-18.png|''Labelmap LUTs'' -[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels|Brain Labels]]: Label colors for brain segmentation -[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010LabelColors|Label Colors]]: Colors for a generic labelmap
file:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs'' -[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors]] -[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]]
</gallery>

==LUTs for Charting==
Please see the [[Slicer4:2012_GenericChartColors|Generic Chart Colors]] page.

==LUTs in Slicer==
You can review and edit LUTs in Slicer via the [[Documentation/{{documentation/version}}/Modules/Colors|Colors module]].
=Slicer ColorPicker=
The slicer colorpicker allows to select colors from a label map and to assign them to objects such as surface models or streamlines.
[[Image:SlicerColorPicker-2012-02-18.png|200px|left]]

==Custom LUTs==
It is relatively easy to create custom LUTs by creating a table with the colors on the wiki. This allows to select specific names and colors when segmenting. See below for an example.

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
|0
|background
|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
|
|-
|1
|tissue
|style="background:rgb(128,174,128)"|rgb(128,174,128)
| Default label for bodily tissues
|-
|2
|bone
|style="background:rgb(241,214,145)"|rgb(241,214,145)
|
|-
|3
|skin
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|4
|connective tissue
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|
|-
|}

* Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
* Go [http://labelpage.halle.us/ here] to create a text file in Slicer LUT format.
* A custom LUT can be loaded into Slicer like any other file.

===Custom LUT Examples===

*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/AbdominalAtlasLabels|Abdominal Atlas Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNAtlasLabels|Head and Neck Atlas Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNLabels|Head and Neck Muscles Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/FemalePelvisColors|Female Pelvis Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/KneeAtlasLabels|Knee Atlas Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Lauras-labels|Laura's Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Mori-Atlas_labels|Mori-Atlas Labels]]

====Brain Atlas LUTs====
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/CCA:Atlases:MRI_Brain_Atlas_2012:ColorFile|2012 Multi-modality MRI-based Atlas of the Brain]]: Good example of the wiki-based labelpage format, including multiple tables.
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/TractographyColors|Tractography Colors]]: LUT for White Matter Parcellation.
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2012SPL-BrainAtlasColorFile|2012 SPL Brain Atlas Colors]]


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==Useful Links==
*Converting wiki pages to and from LUTs
**Web-based tools that convert between wiki and Slicer color files can be found at http://labelpage.halle.us/
*Creating custom palettes: http://colorbrewer2.org/

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@@ Line 9: / Line 9: @@
 file:Shade-LUTs-2012-02-18.png|''Shade LUTs''
 file:Tint-LUTs-2012-02-18.png|''Tint LUTs''
-file:Freesurfer-LUTs-2012-02-18.png|''Freesurfer LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]]
+file:Freesurfer-LUTs-2012-02-18.png|''Freesurfer LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels documentation]]
 file:PET-LUTs-2012-02-18.png|''PET LUTs''
 file:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
-file:Labelmap-LUTs-2012-02-18.png|''Labelmap LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels|Brain Labels]]: Label colors for brain segmentation<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010LabelColors|Label Colors]]: Colors for a generic labelmap
+file:Slicer43-Colors-FromFile.jpeg|''Labelmap LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels|Brain Labels]]: Label colors for brain segmentation<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010LabelColors|Label Colors]]: Colors for a generic labelmap
 file:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors]]<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]]
 </gallery>

Documentation/4.3/SlicerApplication/LookupTables - Revision history

Nicole at 19:09, 15 November 2013

UpdateBot: Nightly -> 4.3