Difference between revisions of "Documentation/4.1/SlicerApplication/LookupTables"

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=Overview=
 
=Overview=
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Slicer offers a variety of predefined lookup tables (LUT). Volumes can be associated with a LUT in the volumes module. Also, [[Documentation/4.0/Modules/Colors|see the colors module]].
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In Slicer, the simplest and most widespread application of medicine-specific knowledge are the color lookup tables (LUT) that Slicer uses to map the integer values contained in label map images into structure names and colors. We have begun to use this wiki as both a centralized repository for lookup table information as well as a collaborative tool for creating new mappings. The following wiki pages are in a special format that allows conversion into Slicer lookup tables. Slicer offers a variety of predefined lookup tables (LUT). Volumes can be associated with a LUT in the volumes module. Also, see the [[Documentation/4.1/Modules/Colors|Colors Module]].
  
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=LUTs=
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==LUTs==
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<gallery widths=200px>
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<gallery widths=175px>
 
file:DiscreteLUTs-2012-02-18.png|''Discrete LUTs''
 
file:DiscreteLUTs-2012-02-18.png|''Discrete LUTs''
 
file:Shade-LUTs-2012-02-18.png|''Shade LUTs''
 
file:Shade-LUTs-2012-02-18.png|''Shade LUTs''
 
file:Tint-LUTs-2012-02-18.png|''Tint LUTs''
 
file:Tint-LUTs-2012-02-18.png|''Tint LUTs''
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file:Freesurfer-LUTs-2012-02-18.png|''Freesurfer LUTs''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:Freesurfer_labels|Freesurfer labels]]
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file:Freesurfer-LUTs-2012-02-18.png|''Freesurfer LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]]
 
file:PET-LUTs-2012-02-18.png|''PET LUTs''
 
file:PET-LUTs-2012-02-18.png|''PET LUTs''
 
file:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
 
file:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
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file:Labelmap-LUTs-2012-02-18.png|''Labelmap LUTs''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:2010_Brain_Labels|2010 Brain Labels]]: Label colors for brain segmentation<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:2010_Label_Colors|2010 Label Colors]]: Colors for a generic labelmap
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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
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file:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]]: default LUT<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:GenericColors.txt|GenericColors]]
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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>
 
</gallery>
  
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===Custom LUTs===
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==LUTs for Charting==
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*[[Slicer3:Mori-Atlas_labels|Mori-Atlas labels]]
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Please see the [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericChartColors|Generic Chart Colors]] page.
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*[[Slicer3:Lauras_labels|Lauras labels]]
 
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*[[CCA:Atlases:MRI_Brain_Atlas_2010:ColorFile|2010 Brain Atlas]]:Good example of the wiki-based labelpage format, including multiple tables.
 
  
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===LUTs for Charting===
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==LUTs in Slicer==
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Please see the [[Slicer4:2012_GenericChartColors|separate page]]
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You can review and edit LUTs in Slicer via the [[Documentation/{{documentation/version}}/Modules/Colors|Colors module]].
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=Slicer ColorPicker=
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The slicer colorpicker allows to select colors from a label map and to assign them to objects such as surface models or streamlines.
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[[Image:SlicerColorPicker-2012-02-18.png|200px|left]]
  
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=LUTs in Slicer=
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==LUTs for Slicer4==
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You can review and edit LUTs in Slicer via the [[Documentation/{{documentation/version}}/Modules/Colors|Colors module]]  
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors LUT for Slicer {{documentation/version}}]]
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=Slicer ColorPicker=
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]]
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[[Image:SlicerColorPicker-2012-02-18.png|300px|right|thumb|The slicer colorpicker allows to select colors from a label map and to assign them to objects such as surface models or streamlines]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels|Brain Labels]]: Short Brain LUT for Slicer General Applications
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010LabelColors|Label Colors]]: Short LUT for Slicer General Applications
  
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=Custom LUTs=
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==Brain Atlas LUTs==
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*[[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.
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/TractographyColors|Tractography Colors]]: LUT for White Matter Parcellation.
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2012SPL-BrainAtlasColorFile|2012 SPL Brain Atlas Colors]]
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==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.
 
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.
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{| class="wikitable sortable labelpage labelpagetable" border="1"
 
{| class="wikitable sortable labelpage labelpagetable" border="1"
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* Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
 
* Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
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* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
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* 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.
 
* A custom LUT can be loaded into Slicer like any other file.
  
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===Custom LUT Examples===
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*[[Documentation/4.1/SlicerApplication/LookupTables/AbdominalAtlasLabels|Abdominal Atlas Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNAtlasLabels|Head and Neck Atlas Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNLabels|Head and Neck Muscles Labels]]
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*[[Documentation/4.1/SlicerApplication/LookupTables/FemalePelvisColors|Female Pelvis Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]]
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*[[Documentation/4.1/SlicerApplication/LookupTables/KneeAtlasLabels|Knee Atlas Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Lauras-labels|Laura's Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Mori-Atlas_labels|Mori-Atlas Labels]]
  
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==Useful Links==
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*Converting wiki pages to and from LUTs
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**Web-based tools that convert between wiki and Slicer color files can be found at  http://labelpage.halle.us/
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*Creating custom palettes: http://colorbrewer2.org/
 
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Latest revision as of 07:28, 14 June 2013

Home < Documentation < 4.1 < SlicerApplication < LookupTables


For the latest Slicer documentation, visit the read-the-docs.



Overview

In Slicer, the simplest and most widespread application of medicine-specific knowledge are the color lookup tables (LUT) that Slicer uses to map the integer values contained in label map images into structure names and colors. We have begun to use this wiki as both a centralized repository for lookup table information as well as a collaborative tool for creating new mappings. The following wiki pages are in a special format that allows conversion into Slicer lookup tables. Slicer offers a variety of predefined lookup tables (LUT). Volumes can be associated with a LUT in the volumes module. Also, see the Colors Module.

LUTs

LUTs for Charting

Please see the Generic Chart Colors page.

LUTs in Slicer

You can review and edit LUTs in Slicer via the 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.

SlicerColorPicker-2012-02-18.png

LUTs for Slicer4

Brain Atlas LUTs

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.

integer_label text_label color notes
0 background rgba(0,0,0,0)
1 tissue rgb(128,174,128) Default label for bodily tissues
2 bone rgb(241,214,145)
3 skin rgb(177,122,101)
4 connective tissue rgb(111,184,210)


Custom LUT Examples

Useful Links

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