Difference between revisions of "Documentation/4.1/SlicerApplication/LookupTables"
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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'' | ||
| − | file:Labelmap-LUTs-2012-02-18.png|''Labelmap LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels| | + | 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:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs''<br>-[[Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors]]<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]] | file:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs''<br>-[[Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors]]<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]] | ||
</gallery> | </gallery> | ||
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors LUT for Slicer {{documentation/version}}]] | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors LUT for Slicer {{documentation/version}}]] | ||
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]] | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]] | ||
| + | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels|Brain Labels]]: Short Brain LUT for Slicer General Applications | ||
| + | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010LabelColors|Label Colors]]: Short LUT for Slicer General Applications | ||
==Brain Atlas LUTs== | ==Brain Atlas LUTs== | ||
| − | *[[CCA:Atlases: | + | *[[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/ | + | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/TractographyColors|Tractography Colors]]: LUT for White Matter Parcellation. |
| − | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/ | + | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2012SPL-BrainAtlasColorFile|2012 SPL Brain Atlas Colors]] |
| − | |||
==Custom 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. | 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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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Lauras-labels|Laura's Labels]] | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Lauras-labels|Laura's Labels]] | ||
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]] | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]] | ||
| + | *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNLabels|Head and Neck Muscles Labels]] | ||
==Useful Links== | ==Useful Links== | ||
Revision as of 22:32, 28 August 2012
Home < Documentation < 4.1 < SlicerApplication < LookupTables
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
Discrete LUTs
Shade LUTs
Tint LUTs
Freesurfer LUTs
-Freesurfer Labels
PET LUTs
Cartilage MRI LUTs
Labelmap LUTs
-Brain Labels: Label colors for brain segmentation
-Label Colors: Colors for a generic labelmap
Generic Labelmap LUTs
-Default Generic Anatomy Colors
-Generic Colors
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.
LUTs for Slicer4
- Default Generic Anatomy Colors LUT for Slicer 4.1
- Generic Colors
- Brain Labels: Short Brain LUT for Slicer General Applications
- Label Colors: Short LUT for Slicer General Applications
Brain Atlas LUTs
- 2012 Multi-modality MRI-based Atlas of the Brain: Good example of the wiki-based labelpage format, including multiple tables.
- Tractography Colors: LUT for White Matter Parcellation.
- 2012 SPL Brain Atlas Colors
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) |
- Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
- Go 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
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/
