Documentation/Nightly/SlicerApplication/LookupTables - Revision history

Mehrtash: /* Custom LUT Examples */

2015-03-04T20:40:22Z

Custom LUT Examples

Nicole: /* LUTs */

2013-11-14T20:04:32Z

LUTs

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:56:24Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

Marianna at 18:11, 19 December 2012

2012-12-19T18:11:27Z

Marianna at 18:11, 19 December 2012

2012-12-19T18:11:00Z

JChris.FillionR: 4.1 -> Nightly

2012-08-22T17:01:32Z

4.1 -> Nightly

New page

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


=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/4.1/Modules/Colors|Colors Module]].

==LUTs==
<gallery widths=200px>
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''     [[Slicer3: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''     [[Slicer3:2010_Brain_Labels|2010 Brain Labels]]: Label colors for brain segmentation     [[Slicer3:2010_Label_Colors|2010 Label Colors]]: Colors for a generic labelmap
file:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs''     [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]]: default LUT     [[Slicer3:GenericColors.txt|GenericColors]]
</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===
*[[Slicer3:Mori-Atlas_labels|Mori-Atlas Labels]]
*[[Slicer3:Lauras_labels|Laura's Labels]]
*[[CCA:Atlases:MRI_Brain_Atlas_2010:ColorFile|2010 Brain Atlas]]: Good example of the wiki-based labelpage format, including multiple tables.
*[[Documentation/{{documentation/version}}/SlicerApplication/LUTs/TractographyColors|Tractography Colors]] LUT for WM Parcellation.


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

@@ Line 75: / Line 75: @@
 *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Lauras-labels|Laura's Labels]]
 *[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Mori-Atlas_labels|Mori-Atlas Labels]]
+*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/PCampReview|PCampReview 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.

@@ 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>

← Older revision		Revision as of 07:56, 14 June 2013
Line 1:		Line 1:
		+	<noinclude>{{documentation/versioncheck}}</noinclude>
	__NOTOC__		__NOTOC__
	=Overview=		=Overview=

← Older revision		Revision as of 18:11, 19 December 2012
Line 1:		Line 1:
		+	__NOTOC__
	=Overview=		=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]].		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]].

@@ Line 1: / Line 1: @@
 =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/4.1/Modules/Colors|Colors Module]].
+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=200px>
+<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''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:Freesurfer_labels|Freesurfer labels]]
+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:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
-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
+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>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]]: default LUT<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Slicer3:GenericColors.txt|GenericColors]]
+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>
@@ Line 63: / Line 58: @@
 |-
 |}
 * Standard color names and values: http://www.w3.org/TR/SVG/types.html#ColorKeywords
@@ Line 70: / Line 64: @@
 ===Custom LUT Examples===
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/slicerapplication-footer}}
 <!-- ---------------------------- -->