Difference between revisions of "Documentation/4.0/SlicerApplication/LookupTables"

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=Overview=
 
=Overview=
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Slicer offers a variety of predefined lookup tables (LUT).
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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]].
  
 
=LUTs=
 
=LUTs=
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<gallery>
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<gallery widths=200px>
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file:DiscreteLUTs-2012-02-18.png|Discrete Luts
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file:DiscreteLUTs-2012-02-18.png|''Discrete LUTs''
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file:Shade-LUTs-2012-02-18.png|Shade Luts
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file:Shade-LUTs-2012-02-18.png|''Shade LUTs''
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file:Tint-LUTs-2012-02-18.png|Tint Luts
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file:Tint-LUTs-2012-02-18.png|''Tint LUTs''
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file:Freesurfer-LUTs-2012-02-18.png|Freesurfer 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:PET-LUTs-2012-02-18.png|PET Luts
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file:PET-LUTs-2012-02-18.png|''PET LUTs''
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file:CartilageMRI-LUTs-2012-02-18.png|Cartilage MRI Luts
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file:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
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file:Labelmap-LUTs-2012-02-18.png|Labelmap 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:GenericLabel-LUTs-2012-02-18.png|Generic Labelmap Luts
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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]]
 
</gallery>
 
</gallery>
  
 +
===Custom LUTs===
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*[[Slicer3:Mori-Atlas_labels|Mori-Atlas labels]]
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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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Please see the [[Slicer4:2012_GenericChartColors|separate page]]
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 +
=LUTs in Slicer=
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You can review and edit LUTs in Slicer via the [[Documentation/{{documentation/version}}/Modules/Colors|Colors module]]
 
=Slicer ColorPicker=
 
=Slicer ColorPicker=
 
[[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]]
 
[[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]]
−
 
−
=LUTs for Charting=
 
−
Please see the [[Slicer4:2012_GenericChartColors|separate page]]
 
  
 
=Custom LUTs=
 
=Custom LUTs=
−
It is relatively easy to create custom LUTs by creating a table with the colors on the wiki. See the example below.
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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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! notes
 
! notes
 
|-
 
|-
−
| 0
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|0
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| background
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|background
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| rgba(0,0,0,0.0)
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|style="background:rgb(0,0,0);color:white"|rgba(0,0,0,0)
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| The background label is included here because it isn't an anatomical structure.
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|
 +
|-
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|1
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|tissue
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|style="background:rgb(128,174,128)"|rgb(128,174,128)
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| Default label for bodily tissues
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|-
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|2
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|bone
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|style="background:rgb(241,214,145)"|rgb(241,214,145)
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|
 +
|-
 +
|3
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|skin
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|style="background:rgb(177,122,101)"|rgb(177,122,101)
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|
 +
|-
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|4
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|connective tissue
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|style="background:rgb(111,184,210)"|rgb(111,184,210)
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|
 +
|-
 
|}
 
|}
  
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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
 
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
 
* [http://labelpage.halle.us/ Go here] to create a text file in Slicer LUT format.
 +
* A custom LUT can be loaded into Slicer like any other file.
  
  

Latest revision as of 07:33, 14 June 2013

Home < Documentation < 4.0 < SlicerApplication < LookupTables


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



Overview

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

Custom LUTs

LUTs for Charting

Please see the separate 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

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)


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