Documentation/4.1/Developers/Sandbox

2013-04-22T14:35:31Z

Halazar: added youtube examples

Documentation/4.2/Training

2012-11-05T14:56:07Z

Halazar:

__TOC__

=Introduction: Slicer {{documentation/version}} Tutorials=

*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
*For questions related to the Slicer4 Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]'''

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome-tutorial_SoniaPujol.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want a general introduction to Slicer.
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|width="100%"
|
*The [[media:Slicer4minute-tutorial_SoniaPujol-mj.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.0.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
|align="right"|
[[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
|}

==Slicer4 Data Loading and 3D Visualization ==
{|width="100%"
|
*The [[Media:DataLoadingAndVisualizationSlicer4.1_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .
*Author: Sonia Pujol, Ph.D.
*Audience: End-users
*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
|align="right"|
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
|}

=Tutorials for software developers=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [[Media:Slicer4_ProgrammingTutorial_SPujol-SPieper.pdf | Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*The [[Media:HelloPythonSlicer4.zip‎| HelloPython dataset]] contains three Python files and an MR scan of the brain.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|width="100%"
|
*The [[Media:DiffusionTensorImaging_Slicer4.1_SoniaPujol.pdf | Diffusion Tensor Imaging Tutorial]] course guides through the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts.
*Author: Sonia Pujol, Ph.D.
*Audience: End-users and developers
*The [[Media:DiffusionMRI_tutorialData.zip |DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
|align="right"|
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
|}

==Slicer4 Neurosurgical Planning Tutorial==
{|width="100%"
|
*The [[Media:NeurosurgicalPlanning_SoniaPujol.pdf | Neurosurgical Planning tutorial]] course guides through the generation of fiber tracts in the vicinity of a tumor.
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
*Audience: End-users and developers
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DVisualizationDICOMforRadiologyApplications_SoniaPujol_KittShaffer_RSNA2011.pdf | Slicer4RSNA]] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
*The [[Media:3DVisualizationData RSNA2011 part1.zip | Slicer4RSNAdataset1]] and [[Media:3DVisualizationData RSNA2011 part2.zip | Slicer4RSNAdataset2]] contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
|align="right"|
[[Image:Slicer4RSNA_2.png|right|250px|]]
|}

==Slicer4 Quantitative Imaging tutorial==
{|width="100%"
|
*The [[media:Slicer4QuantitativeImaging.pdf| Slicer4 Quantitative Imaging tutorial]] guides through the use for Slicer for quantifying small volumetric changes in slow-growing tumors, and for calculating Standardized Uptake Value (SUV) from PET/CT data.
*Authors: Jeffrey Yap, Ph.D., Ron Kikinis, M.D., Randy Gollub, M.D., Ph.D., Wendy Plesniak, Ph.D., Nicole Aucoin, B.Sc., Sonia Pujol, Ph.D., Valerie Humblet, Ph.D., Andriy Fedorov, Ph.D., Kilian Poh, Ph.D., Ender Konugolu, Ph.D.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
*The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
|align="right"|
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
|}

=Summer 2012 Tutorial contest (under construction)=

==Automatic Left Atrial Scar Segmenter ==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
*Authors: Greg Gardner, Josh Cates, SCI, Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
|align="right"|
|}

==Qualitative and quantitative comparison of two RT dose distributions==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions]
*Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH
|align="right"|
|}

==Dose accumulation for adaptive radiation therapy==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
*Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
|align="right"|
|}

==WebGL Export==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf WebdGLExport]
*Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
|align="right"|
|}

==OpenIGTLink==
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
|}

=Additional resources =
{|width="100%"
|
* This ''Slicer 4.1 [http://vimeo.com/41096643 webinar]'' presents the new features and improvements of the release, and a brief overview of work for the next release.
* Authors: Steve Pieper Ph.D.
* Audience: First time users and developers interested in Slicer 4.1 new features.
* Length: 0h20m
|align="right"|[[Image:Webinar-Slicer-4.1.png|250px]]
|-
|
*This ''Intro to Slicer 4.0 [http://vimeo.com/37671358 webinar]'' provides an introduction to 3DSlicer, and demonstrates core functionalities such as loading, visualizing and saving data. Basic processing tools, including manual registration, manual segmentation and tractography tools are also highlighted. This webinar is a general overview. For in depth information see the modules above and the documentation pages.
*Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S.
*Audience: First time users interested in a broad overview of Slicer’s features and tools.
*Length: 1h20m
|align="right"|[[Image:Webinar.png|250px]]
|-
|
*The ''[http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable Slicer Registration Case Library]'' provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself.
:Author: Dominik Meier, Ph.D.
:Audience: users interested learning/applying Slicer image registration technology
|align="right"|[[Image:RegLib Banner.png|250px]]
|}

Documentation/Nightly/Developers/Modules

2012-09-24T03:16:08Z

Halazar:

Slicer supports three types of modules. While the developer has to choose between one of the three types to implement its module, the end user won't notice the difference as they all share the same look & feel. The choice for a given type of module is usually based on the type of inputs/parameters for a given module.

= Command Line Interface (CLI) =
CLIs are standalone executables with a limited input/output arguments complexity (simple argument types, no user interactions...). They are typically implemented using [http://www.itk.org ITK].
* Shared lib or executable
* UI automatically generated
* Where to start ?
# Create initial skeleton using [[Documentation/{{documentation/version}}/Developers/ModuleWizard|module wizard]]
# Read [[Documentation/{{documentation/version}}/Developers/Build_Module|Compiling slicer modules outside of the slicer source tree.]]
# Learn from existing [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ existing modules]
* Links:
** [[Slicer3:Execution_Model_Documentation|Slicer3 execution model]] (Slicer4 is very similar)
** [http://www.na-mic.org/Wiki/index.php/File:Slicer4_CLI.ppt CLI in Slicer4] (presentation of 2012 NAMIC AHM)

= Loadable Modules =
Loadable modules are [http://en.wikipedia.org/wiki/C%2B%2B C++] plugins that are built against Slicer. They define custom GUIs for their specific behavior as they have full control over the application.
* C++ shared library
* Full control over the UI (based on [http://qt.nokia.com/products/ Qt]) and Slicer internals (MRML, logics, display managers...)
* Optimized for heavy computations
* Where to start ?
# Create initial skeleton using [[Documentation/{{documentation/version}}/Developers/ModuleWizard|module wizard]]
# Read [[Documentation/{{documentation/version}}/Developers/Build_Module|Compiling slicer modules outside of the slicer source tree.]]
# Learn from existing [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/ existing modules]
* Links:
**[http://www.na-mic.org/Wiki/index.php/File:LoadableModules.pptx Loadable modules] (presentation of 2012 NAMIC AHM)
**[[Documentation/{{documentation/version}}/Developers/Tutorials/CreateLoadableModule|How to write a loadable module]]

= Scripted Modules =
Scripted modules are written in [http://www.python.org/ Python] and typically but not necessarily use the high level API of Slicer and toolkits.
* Python Console
* Full access to the API: [http://www.vtk.org VTK], [http://www.itk.org ITK], MRML, [http://qt.nokia.com/products/ Qt] and Slicer are fully wrapped
* Recommended for fast prototyping
* Where to start ?
# Create initial skeleton using [[Documentation/{{documentation/version}}/Developers/ModuleWizard|module wizard]]
# Read [[Documentation/{{documentation/version}}/Developers/Build_Module|Compiling slicer modules outside of the slicer source tree.]]
# Learn from existing [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/ existing modules]
* Links:
** [http://www.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Developers/Python_scripting Python Scripting]
** [[Documentation/{{documentation/version}}/Training#Slicer4_Programming_Tutorial|Python Scripting Tutorial]]

=Module Factory=
Loading modules into slicer happens in multiple steps:
*module factories must be registered into the factory manager
* directories where the modules to load are located must be passed to the factory manager
* Optionally specify module names to ignore
* scan the directories and test which file is a module and register it (not instantiated yet)
* Instantiate all the register modules
* Connect each module with the scene and the application
More details can be found in the [http://slicer.org/doc/html/classqSlicerAbstractModuleFactoryManager.html online doc]

==ToDo==
* Transform all core modules into Loadable modules.
** the factory manager only support file based modules, core modules are not file based (linked into the core factory itself)
* Move factory registration in qSlicerApplication (or a general application library) to support module discovery/loading without needing to instantiate Slicer.
** Currently can't be moved into qSlicerApplication as the CLI factories that are in QTCLI depend on QTGUI
** QtTesting is also limited with the QTCLI dependency on QtGUI (->qSlicerApplication would need to access QtTesting code from QtCli)
** Proposed architecture
Base
Application -> classes that are useful to build an application (mix of qSlicerCoreApplication, qSlicerApplication, Main.cxx...)
Core -> formally QtCore
Modules -> contains the factories and module specific code
Loadable
CLI
Scripted
Scripted -> all that is python specific
Cxx
Python
Widgets -> formally QtGUI
* Add category hierarchy in the Settings module panel
* Register factory settings/command-options(e.g. disable-loadable-modules) when registering module factories
** To have the settings panel be generic but have the code proper of each registered factory somewhere else
* Add mechanism for modules to register dialogs (toolbars that open dialogs), e.g. the sceneview module needs to register the sceneView dialog into an icon.
* Ignore modules from the launcher command line.
* cloning" of module panels at run time. See [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008965.html "here] and [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008039.html here]

File:3DSlicerQtTesting.gif

2012-07-24T17:12:28Z

Halazar: uploaded a new version of "File:3DSlicerQtTesting.gif": Reverted to version as of 19:01, 23 May 2012

File:3DSlicerQtTesting.gif

2012-07-24T16:56:58Z

Halazar: uploaded a new version of "File:3DSlicerQtTesting.gif": See if thumbail is generated....

Slicer3:2010 GenericAnatomyColors

2011-09-15T14:17:24Z

Halazar: put "unknown" back at a new label value (308)

__NOTOC__

[[Slicer3:LUTs_and_Ontologies|Back to LUT and ontologies page]]

*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.
* If changing the order of the table, the indices can be recreated with [[Slicer3:LUTs_and_Ontologies:Renumber_Script|this tcl script]].
2010 Generic Anatomy Colors for use with the Slicer3 Editor Module as a default color table for editing medical image data with no prior knowledge of the condition, modality, or specific anatomical region being displayed. When additional protocol knowledge is available (i.e. angiography of the brain) a different color table with more specific labels may be chosen.

Authors: Michael Halle, Florin Talos, Ron Kikinis, Steve Pieper, Nicole Aucoin.

==Lookup table==

{| 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)
|
|-
|5
|blood
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|
|-
|6
|organ
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|
|-
|7
|mass
|style="background:rgb(144,238,144)"|rgb(144,238,144)
| Could be tumor or other lesion
|-
|8
|muscle
|style="background:rgb(192,104,88)"|rgb(192,104,88)
|
|-
|9
|foreign object
|style="background:rgb(220,245,20)"|rgb(220,245,20)
| Implants, surical instruments, table...
|-
|10
|waste
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|
|-
|11
|teeth
|style="background:rgb(255,250,220)"|rgb(255,250,220)
|
|-
|12
|fat
|style="background:rgb(230,220,70)"|rgb(230,220,70)
|
|-
|13
|gray matter
|style="background:rgb(200,200,235)"|rgb(200,200,235)
|
|-
|14
|white matter
|style="background:rgb(250,250,210)"|rgb(250,250,210)
|
|-
|15
|nerve
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|16
|vein
|style="background:rgb(0,151,206)"|rgb(0,151,206)
|
|-
|17
|artery
|style="background:rgb(216,101,79)"|rgb(216,101,79)
|
|-
|18
|capillary
|style="background:rgb(183,156,220)"|rgb(183,156,220)
|
|-
|19
|ligament
|style="background:rgb(183,214,211)"|rgb(183,214,211)
|
|-
|20
|tendon
|style="background:rgb(152,189,207)"|rgb(152,189,207)
|
|-
|21
|cartilage
|style="background:rgb(111,184,210)"|rgb(111,184,210)
|
|-
|22
|meniscus
|style="background:rgb(178,212,242)"|rgb(178,212,242)
|
|-
|23
|lymph node
|style="background:rgb(68,172,100)"|rgb(68,172,100)
|
|-
|24
|lymphatic vessel
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|
|-
|25
|cerebro-spinal fluid
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|26
|bile
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|27
|urine
|style="background:rgb(214,230,130)"|rgb(214,230,130)
|
|-
|28
|feces
|style="background:rgb(78,63,0)"|rgb(78,63,0)
|
|-
|29
|gas
|style="background:rgb(218,255,255)"|rgb(218,255,255)
|
|-
|30
|fluid
|style="background:rgb(170,250,250)"|rgb(170,250,250)
|
|-
|31
|edema
|style="background:rgb(140,224,228)"|rgb(140,224,228)
|
|-
|32
|bleeding
|style="background:rgb(188,65,28)"|rgb(188,65,28)
|
|-
|33
|necrosis
|style="background:rgb(216,191,216)"|rgb(216,191,216)
|
|-
|34
|clot
|style="background:rgb(145,60,66)"|rgb(145,60,66)
|
|-
|35
|embolism
|style="background:rgb(150,98,83)"|rgb(150,98,83)
|
|-
|36
|head
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|37
|central nervous system
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|38
|brain
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|39
|gray matter of brain
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|40
|telencephalon
|style="background:rgb(68,131,98)"|rgb(68,131,98)
|
|-
|41
|cerebral cortex
|style="background:rgb(128,174,128)"|rgb(128,174,128)
|
|-
|42
|right frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|43
|left frontal lobe
|style="background:rgb(83,146,164)"|rgb(83,146,164)
|
|-
|44
|right temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|45
|left temporal lobe
|style="background:rgb(162,115,105)"|rgb(162,115,105)
|
|-
|46
|right parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|47
|left parietal lobe
|style="background:rgb(141,93,137)"|rgb(141,93,137)
|
|-
|48
|right occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|49
|left occipital lobe
|style="background:rgb(182,166,110)"|rgb(182,166,110)
|
|-
|50
|right insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|51
|left insular lobe
|style="background:rgb(188,135,166)"|rgb(188,135,166)
|
|-
|52
|right limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|53
|left limbic lobe
|style="background:rgb(154,150,201)"|rgb(154,150,201)
|
|-
|54
|right striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|55
|left striatum
|style="background:rgb(177,140,190)"|rgb(177,140,190)
|
|-
|56
|right caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|57
|left caudate nucleus
|style="background:rgb(30,111,85)"|rgb(30,111,85)
|
|-
|58
|right putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|59
|left putamen
|style="background:rgb(210,157,166)"|rgb(210,157,166)
|
|-
|60
|right pullidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|61
|left pallidum
|style="background:rgb(48,129,126)"|rgb(48,129,126)
|
|-
|62
|right amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|63
|left amygdaloid complex
|style="background:rgb(98,153,112)"|rgb(98,153,112)
|
|-
|64
|diencephalon
|style="background:rgb(69,110,53)"|rgb(69,110,53)
|
|-
|65
|thalamus
|style="background:rgb(166,113,137)"|rgb(166,113,137)
|
|-
|66
|right thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|67
|left thalamus
|style="background:rgb(122,101,38)"|rgb(122,101,38)
|
|-
|68
|pineal gland
|style="background:rgb(253,135,192)"|rgb(253,135,192)
|
|-
|69
|midbrain
|style="background:rgb(145,92,109)"|rgb(145,92,109)
|
|-
|70
|substantia nigra
|style="background:rgb(46,101,131)"|rgb(46,101,131)
|
|-
|71
|right substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|72
|left substantia nigra
|style="background:rgb(0,108,112)"|rgb(0,108,112)
|
|-
|73
|cerebral white matter
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|74
|right superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|75
|left superior longitudinal fasciculus
|style="background:rgb(127,150,88)"|rgb(127,150,88)
|
|-
|76
|right inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|77
|left inferior longitudinal fasciculus
|style="background:rgb(159,116,163)"|rgb(159,116,163)
|
|-
|78
|right arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|79
|left arcuate fasciculus
|style="background:rgb(125,102,154)"|rgb(125,102,154)
|
|-
|80
|right uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|81
|left uncinate fasciculus
|style="background:rgb(106,174,155)"|rgb(106,174,155)
|
|-
|82
|right cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|83
|left cingulum bundle
|style="background:rgb(154,146,83)"|rgb(154,146,83)
|
|-
|84
|projection fibers
|style="background:rgb(126,126,55)"|rgb(126,126,55)
|
|-
|85
|right corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|86
|left corticospinal tract
|style="background:rgb(201,160,133)"|rgb(201,160,133)
|
|-
|87
|right optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|88
|left optic radiation
|style="background:rgb(78,152,141)"|rgb(78,152,141)
|
|-
|89
|right medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|90
|left medial lemniscus
|style="background:rgb(174,140,103)"|rgb(174,140,103)
|
|-
|91
|right superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|92
|left superior cerebellar peduncle
|style="background:rgb(139,126,177)"|rgb(139,126,177)
|
|-
|93
|right middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|94
|left middle cerebellar peduncle
|style="background:rgb(148,120,72)"|rgb(148,120,72)
|
|-
|95
|right inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|96
|left inferior cerebellar peduncle
|style="background:rgb(186,135,135)"|rgb(186,135,135)
|
|-
|97
|optic chiasm
|style="background:rgb(99,106,24)"|rgb(99,106,24)
|
|-
|98
|right optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|99
|left optic tract
|style="background:rgb(156,171,108)"|rgb(156,171,108)
|
|-
|100
|right fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|101
|left fornix
|style="background:rgb(64,123,147)"|rgb(64,123,147)
|
|-
|102
|commissural fibers
|style="background:rgb(138,95,74)"|rgb(138,95,74)
|
|-
|103
|corpus callosum
|style="background:rgb(97,113,158)"|rgb(97,113,158)
|
|-
|104
|posterior commissure
|style="background:rgb(126,161,197)"|rgb(126,161,197)
|
|-
|105
|cerebellar white matter
|style="background:rgb(194,195,164)"|rgb(194,195,164)
|
|-
|106
|CSF space
|style="background:rgb(85,188,255)"|rgb(85,188,255)
|
|-
|107
|ventricles of brain
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|108
|right lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|109
|left lateral ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|110
|right third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|111
|left third ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|112
|cerebral aqueduct
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|113
|fourth ventricle
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|114
|subarachnoid space
|style="background:rgb(88,106,215)"|rgb(88,106,215)
|
|-
|115
|spinal cord
|style="background:rgb(244,214,49)"|rgb(244,214,49)
|
|-
|116
|gray matter of spinal cord
|style="background:rgb(200,200,215)"|rgb(200,200,215)
|
|-
|117
|white matter of spinal cord
|style="background:rgb(250,250,225)"|rgb(250,250,225)
|
|-
|118
|endocrine system of brain
|style="background:rgb(82,174,128)"|rgb(82,174,128)
|
|-
|119
|pituitary gland
|style="background:rgb(57,157,110)"|rgb(57,157,110)
|
|-
|120
|adenohypophysis
|style="background:rgb(60,143,83)"|rgb(60,143,83)
|
|-
|121
|neurohypophysis
|style="background:rgb(92,162,109)"|rgb(92,162,109)
|
|-
|122
|meninges
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|123
|dura mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|124
|arachnoid
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|125
|pia mater
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|126
|muscles of head
|style="background:rgb(201,121,77)"|rgb(201,121,77)
|
|-
|127
|salivary glands
|style="background:rgb(70,163,117)"|rgb(70,163,117)
|
|-
|128
|lips
|style="background:rgb(188,91,95)"|rgb(188,91,95)
|
|-
|129
|nose
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|130
|tongue
|style="background:rgb(166,84,94)"|rgb(166,84,94)
|
|-
|131
|soft palate
|style="background:rgb(182,105,107)"|rgb(182,105,107)
|
|-
|132
|right inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|133
|left inner ear
|style="background:rgb(229,147,118)"|rgb(229,147,118)
|
|-
|134
|right external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|135
|left external ear
|style="background:rgb(174,122,90)"|rgb(174,122,90)
|
|-
|136
|right middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|137
|left middle ear
|style="background:rgb(201,112,73)"|rgb(201,112,73)
|
|-
|138
|right eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|139
|left eyeball
|style="background:rgb(194,142,0)"|rgb(194,142,0)
|
|-
|140
|skull
|style="background:rgb(241,213,144)"|rgb(241,213,144)
|
|-
|141
|right frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|142
|left frontal bone
|style="background:rgb(203,179,77)"|rgb(203,179,77)
|
|-
|143
|right parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|144
|left parietal bone
|style="background:rgb(229,204,109)"|rgb(229,204,109)
|
|-
|145
|right temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|146
|left temporal bone
|style="background:rgb(255,243,152)"|rgb(255,243,152)
|
|-
|147
|right sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|148
|left sphenoid bone
|style="background:rgb(209,185,85)"|rgb(209,185,85)
|
|-
|149
|right ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|150
|left ethmoid bone
|style="background:rgb(248,223,131)"|rgb(248,223,131)
|
|-
|151
|occipital bone
|style="background:rgb(255,230,138)"|rgb(255,230,138)
|
|-
|152
|maxilla
|style="background:rgb(196,172,68)"|rgb(196,172,68)
|
|-
|153
|right zygomatic bone
|style="background:rgb(255,255,167)"|rgb(255,255,167)
|
|-
|154
|right lacrimal bone
|style="background:rgb(255,250,160)"|rgb(255,250,160)
|
|-
|155
|vomer bone
|style="background:rgb(255,237,145)"|rgb(255,237,145)
|
|-
|156
|right palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|157
|left palatine bone
|style="background:rgb(242,217,123)"|rgb(242,217,123)
|
|-
|158
|mandible
|style="background:rgb(222,198,101)"|rgb(222,198,101)
|
|-
|159
|neck
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|160
|muscles of neck
|style="background:rgb(213,124,109)"|rgb(213,124,109)
|
|-
|161
|pharynx
|style="background:rgb(184,105,108)"|rgb(184,105,108)
|
|-
|162
|larynx
|style="background:rgb(150,208,243)"|rgb(150,208,243)
|
|-
|163
|thyroid gland
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|164
|right parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|165
|left parathyroid glands
|style="background:rgb(62,162,114)"|rgb(62,162,114)
|
|-
|166
|skeleton of neck
|style="background:rgb(242,206,142)"|rgb(242,206,142)
|
|-
|167
|hyoid bone
|style="background:rgb(250,210,139)"|rgb(250,210,139)
|
|-
|168
|cervical vertebral column
|style="background:rgb(255,255,207)"|rgb(255,255,207)
|
|-
|169
|thorax
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|170
|trachea
|style="background:rgb(182,228,255)"|rgb(182,228,255)
|
|-
|171
|bronchi
|style="background:rgb(175,216,244)"|rgb(175,216,244)
|
|-
|172
|right lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|173
|left lung
|style="background:rgb(197,165,145)"|rgb(197,165,145)
|
|-
|174
|superior lobe of right lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|175
|superior lobe of left lung
|style="background:rgb(172,138,115)"|rgb(172,138,115)
|
|-
|176
|middle lobe of right lung
|style="background:rgb(202,164,140)"|rgb(202,164,140)
|
|-
|177
|inferior lobe of right lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|178
|inferior lobe of left lung
|style="background:rgb(224,186,162)"|rgb(224,186,162)
|
|-
|179
|pleura
|style="background:rgb(255,245,217)"|rgb(255,245,217)
|
|-
|180
|heart
|style="background:rgb(206,110,84)"|rgb(206,110,84)
|
|-
|181
|right atrium
|style="background:rgb(210,115,89)"|rgb(210,115,89)
|
|-
|182
|left atrium
|style="background:rgb(203,108,81)"|rgb(203,108,81)
|
|-
|183
|atrial septum
|style="background:rgb(233,138,112)"|rgb(233,138,112)
|
|-
|184
|ventricular septum
|style="background:rgb(195,100,73)"|rgb(195,100,73)
|
|-
|185
|right ventricle of heart
|style="background:rgb(181,85,57)"|rgb(181,85,57)
|
|-
|186
|left ventricle of heart
|style="background:rgb(152,55,13)"|rgb(152,55,13)
|
|-
|187
|mitral valve
|style="background:rgb(159,63,27)"|rgb(159,63,27)
|
|-
|188
|tricuspid valve
|style="background:rgb(166,70,38)"|rgb(166,70,38)
|
|-
|189
|aortic valve
|style="background:rgb(218,123,97)"|rgb(218,123,97)
|
|-
|190
|pulmonary valve
|style="background:rgb(225,130,104)"|rgb(225,130,104)
|
|-
|191
|aorta
|style="background:rgb(224,97,76)"|rgb(224,97,76)
|
|-
|192
|pericardium
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|193
|pericardial cavity
|style="background:rgb(184,122,154)"|rgb(184,122,154)
|
|-
|194
|esophagus
|style="background:rgb(211,171,143)"|rgb(211,171,143)
|
|-
|195
|thymus
|style="background:rgb(47,150,103)"|rgb(47,150,103)
|
|-
|196
|mediastinum
|style="background:rgb(255,244,209)"|rgb(255,244,209)
|
|-
|197
|skin of thoracic wall
|style="background:rgb(173,121,88)"|rgb(173,121,88)
|
|-
|198
|muscles of thoracic wall
|style="background:rgb(188,95,76)"|rgb(188,95,76)
|
|-
|199
|skeleton of thorax
|style="background:rgb(255,239,172)"|rgb(255,239,172)
|
|-
|200
|thoracic vertebral column
|style="background:rgb(226,202,134)"|rgb(226,202,134)
|
|-
|201
|ribs
|style="background:rgb(253,232,158)"|rgb(253,232,158)
|
|-
|202
|sternum
|style="background:rgb(244,217,154)"|rgb(244,217,154)
|
|-
|203
|right clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|204
|left clavicle
|style="background:rgb(205,179,108)"|rgb(205,179,108)
|
|-
|205
|abdominal cavity
|style="background:rgb(186,124,161)"|rgb(186,124,161)
|
|-
|206
|abdomen
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|207
|peritoneum
|style="background:rgb(255,255,220)"|rgb(255,255,220)
|
|-
|208
|omentum
|style="background:rgb(234,234,194)"|rgb(234,234,194)
|
|-
|209
|peritoneal cavity
|style="background:rgb(204,142,178)"|rgb(204,142,178)
|
|-
|210
|retroperitoneal space
|style="background:rgb(180,119,153)"|rgb(180,119,153)
|
|-
|211
|stomach
|style="background:rgb(216,132,105)"|rgb(216,132,105)
|
|-
|212
|duodenum
|style="background:rgb(255,253,229)"|rgb(255,253,229)
|
|-
|213
|small bowel
|style="background:rgb(205,167,142)"|rgb(205,167,142)
|
|-
|214
|colon
|style="background:rgb(204,168,143)"|rgb(204,168,143)
|
|-
|215
|anus
|style="background:rgb(255,224,199)"|rgb(255,224,199)
|
|-
|216
|liver
|style="background:rgb(221,130,101)"|rgb(221,130,101)
|
|-
|217
|biliary tree
|style="background:rgb(0,145,30)"|rgb(0,145,30)
|
|-
|218
|gallbladder
|style="background:rgb(139,150,98)"|rgb(139,150,98)
|
|-
|219
|pancreas
|style="background:rgb(249,180,111)"|rgb(249,180,111)
|
|-
|220
|spleen
|style="background:rgb(157,108,162)"|rgb(157,108,162)
|
|-
|221
|urinary system
|style="background:rgb(203,136,116)"|rgb(203,136,116)
|
|-
|222
|right kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|223
|left kidney
|style="background:rgb(185,102,83)"|rgb(185,102,83)
|
|-
|224
|right ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|225
|left ureter
|style="background:rgb(247,182,164)"|rgb(247,182,164)
|
|-
|226
|urinary bladder
|style="background:rgb(222,154,132)"|rgb(222,154,132)
|
|-
|227
|urethra
|style="background:rgb(124,186,223)"|rgb(124,186,223)
|
|-
|228
|right adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|229
|left adrenal gland
|style="background:rgb(249,186,150)"|rgb(249,186,150)
|
|-
|230
|female internal genitalia
|style="background:rgb(244,170,147)"|rgb(244,170,147)
|
|-
|231
|uterus
|style="background:rgb(255,181,158)"|rgb(255,181,158)
|
|-
|232
|right fallopian tube
|style="background:rgb(255,190,165)"|rgb(255,190,165)
|
|-
|233
|left fallopian tube
|style="background:rgb(227,153,130)"|rgb(227,153,130)
|
|-
|234
|right ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|235
|left ovary
|style="background:rgb(213,141,113)"|rgb(213,141,113)
|
|-
|236
|vagina
|style="background:rgb(193,123,103)"|rgb(193,123,103)
|
|-
|237
|male internal genitalia
|style="background:rgb(216,146,127)"|rgb(216,146,127)
|
|-
|238
|prostate
|style="background:rgb(230,158,140)"|rgb(230,158,140)
|
|-
|239
|right seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|240
|left seminal vesicle
|style="background:rgb(245,172,147)"|rgb(245,172,147)
|
|-
|241
|right deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|242
|left deferent duct
|style="background:rgb(241,172,151)"|rgb(241,172,151)
|
|-
|243
|skin of abdominal wall
|style="background:rgb(177,124,92)"|rgb(177,124,92)
|
|-
|244
|muscles of abdominal wall
|style="background:rgb(171,85,68)"|rgb(171,85,68)
|
|-
|245
|skeleton of abdomen
|style="background:rgb(217,198,131)"|rgb(217,198,131)
|
|-
|246
|lumbar vertebral column
|style="background:rgb(212,188,102)"|rgb(212,188,102)
|
|-
|247
|female external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|248
|male external genitalia
|style="background:rgb(185,135,134)"|rgb(185,135,134)
|
|-
|249
|skeleton of upper limb
|style="background:rgb(198,175,125)"|rgb(198,175,125)
|
|-
|250
|muscles of upper limb
|style="background:rgb(194,98,79)"|rgb(194,98,79)
|
|-
|251
|right upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|252
|left upper limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|253
|right shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|254
|left shoulder
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|255
|right arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|256
|left arm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|257
|right elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|258
|left elbow
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|259
|right forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|260
|left forearm
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|261
|right wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|262
|left wrist
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|263
|right hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|264
|left hand
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|265
|skeleton of lower limb
|style="background:rgb(255,238,170)"|rgb(255,238,170)
|
|-
|266
|muscles of lower limb
|style="background:rgb(206,111,93)"|rgb(206,111,93)
|
|-
|267
|right lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|268
|left lower limb
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|269
|right hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|270
|left hip
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|271
|right thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|272
|left thigh
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|273
|right knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|274
|left knee
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|275
|right leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|276
|left leg
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|277
|right foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|278
|left foot
|style="background:rgb(177,122,101)"|rgb(177,122,101)
|
|-
|279
|peripheral nervous system
|style="background:rgb(216,186,0)"|rgb(216,186,0)
|
|-
|280
|autonomic nerve
|style="background:rgb(255,226,77)"|rgb(255,226,77)
|
|-
|281
|sympathetic trunk
|style="background:rgb(255,243,106)"|rgb(255,243,106)
|
|-
|282
|cranial nerves
|style="background:rgb(255,234,92)"|rgb(255,234,92)
|
|-
|283
|vagus nerve
|style="background:rgb(240,210,35)"|rgb(240,210,35)
|
|-
|284
|peripheral nerve
|style="background:rgb(224,194,0)"|rgb(224,194,0)
|
|-
|285
|circulatory system
|style="background:rgb(213,99,79)"|rgb(213,99,79)
|
|-
|286
|systemic arterial system
|style="background:rgb(217,102,81)"|rgb(217,102,81)
|
|-
|287
|systemic venous system
|style="background:rgb(0,147,202)"|rgb(0,147,202)
|
|-
|288
|pulmonary arterial system
|style="background:rgb(0,122,171)"|rgb(0,122,171)
|
|-
|289
|pulmonary venous system
|style="background:rgb(186,77,64)"|rgb(186,77,64)
|
|-
|290
|lymphatic system
|style="background:rgb(111,197,131)"|rgb(111,197,131)
|
|-
|291
|needle
|style="background:rgb(240,255,30)"|rgb(240,255,30)
|
|-
|292
|region 0
|style="background:rgb(185,232,61)"|rgb(185,232,61)
|
|-
|293
|region 1
|style="background:rgb(0,226,255)"|rgb(0,226,255)
|
|-
|294
|region 2
|style="background:rgb(251,159,255)"|rgb(251,159,255)
|
|-
|295
|region 3
|style="background:rgb(230,169,29)"|rgb(230,169,29)
|
|-
|296
|region 4
|style="background:rgb(0,194,113)"|rgb(0,194,113)
|
|-
|297
|region 5
|style="background:rgb(104,160,249)"|rgb(104,160,249)
|
|-
|298
|region 6
|style="background:rgb(221,108,158)"|rgb(221,108,158)
|
|-
|299
|region 7
|style="background:rgb(137,142,0)"|rgb(137,142,0)
|
|-
|300
|region 8
|style="background:rgb(230,70,0)"|rgb(230,70,0)
|
|-
|301
|region 9
|style="background:rgb(0,147,0)"|rgb(0,147,0)
|
|-
|302
|region 10
|style="background:rgb(0,147,248)"|rgb(0,147,248)
|
|-
|303
|region 11
|style="background:rgb(231,0,206)"|rgb(231,0,206)
|
|-
|304
|region 12
|style="background:rgb(129,78,0)"|rgb(129,78,0)
|
|-
|305
|region 13
|style="background:rgb(0,116,0)"|rgb(0,116,0)
|
|-
|306
|region 14
|style="background:rgb(0,0,255)"|rgb(0,0,255)
|
|-
|307
|region 15
|style="background:rgb(157,0,0)"|rgb(157,0,0)
|
|-
|308
|unknown
|style="background:rgb(100,100,130)"|rgb(100,100,130)
|
|-
|}

2011-01-25T06:03:32Z

Halazar: old CSF label really pointed to third venticle

__NOTOC__

[[Slicer3:LUTs_and_Ontologies|Back to LUT and ontologies page]]

*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.

[[Category:LabelPage]]
[[Category:LabelPageSlicerColorFile]]
== Title ==
'''NAC CCA Core 2010 MRI Brain Atlas'''
== Description ==
This file contains the label information for the 2010 MRI Brain Atlas from the NAC CCA Core.

== Credits ==
; Authors
: Ion-Florin Talos MD
: Michael Halle PhD

; Institutions
: Center for Computational Anatomy Core, Neuroimage Analysis Center, Surgical Planning Lab, Brigham and Women's Hospital

; Grants
: Neuroimage Analysis Center (NAC), National Institutes of Health (NIH), National Center for Research Resources (NCRR), NIH P41 RR13218.

; Creation Date
: 02/16/2009

== Imports ==

Lookup table information can be imported from other pages by adding links to those pages in a section like this one named "Imports".

The atlas doesn't currently import any such files.

== Lookup table information ==

Any tables defined with class "labelpagetable" in the wiki markup will be interpreted as part of the color file description. The information in the tables are concatenated. For color file construction, the tables need to have columns named "integer_label", "text_label", and "color". These columns can appear in any order. Other columns can be included (for example, "notes").

Multiple tables can be used to organize large sets of labels for efficient viewing and editing.

The "color" column uses either CSS3-type color descriptions or raw integer values to describe the red, green, blue, and possibly alpha values of the color.

=== Non-anatomic entities ===

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
| 0
| background
| rgba(0,0,0,0.0)
| The background label is included here because it isn't an anatomical structure.
|}

=== Atlas lookup table ===
{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! integer_label
! text_label
! color
! radlex_id
! radlex_structure_id
! cca_atlas_id
! notes
|-
| int2
| 2
| white matter of left cerebral hemisphere
| rgb(245,245,245)
| RID16998
| RID16998
|
|
|-
| int4
| 4
| left lateral ventricle
| rgb(88,106,215)
| RID13807
| RID13807
|
|
|-
| int5
| 5
| temporal horn of left lateral ventricle
| rgb(88,106,215)
| RID13803
| RID13803
|
|
|-
| int7
| 7
| white matter of left hemisphere of cerebellum
| rgb(221,248,164)
| RID17313
| RID17313
|
|
|-
| int8
| 8
| left cerebellar cortex
| rgb(230,148,34)
| RID15574
| RID15574
|
|
|-
| int10
| 10
| left thalamus
| rgb(0,118,14)
| RID13496
| RID13496
|
|
|-
| int11
| 11
| left caudate nucleus
| rgb(122,186,220)
| RID21020
| RID21020
|
|
|-
| int12
| 12
| left putamen
| rgb(236,13,176)
| RID21015
| RID21015
|
|
|-
| int13
| 13
| left globus pallidus pars externa
| rgb(12,48,255)
| RID18435
| RID18435
|
|
|-
| int14
| 14
| third ventricle
| rgb(88,106,215)
| RID7137
| RID7137
|
|
|-
| int15
| 15
| fourth ventricle
| rgb(88,106,215)
| RID7147
| RID7147
|
|
|-
| int17
| 17
| left hippocampus
| rgb(220,216,20)
| RID26565
| RID26565
|
|
|-
| int18
| 18
| left amygdala
| rgb(103,255,255)
| RID15698
| RID15698
|
|
|-
| int24
| 24
| third ventricle
| rgb(88,106,215)
| RID7137
| RID7137
|
|
|-
| int25
| 25
| left globus pallidus pars interna
| rgb(255,165,0)
| RID18438
| RID18438
|
|
|-
| int26
| 26
| left nucleus accumbens
| rgb(165,0,255)
| RID21022
| RID21022
|
|
|-
| int27
| 27
| left middle cerebellar peduncle
| rgb(0,255,127)
| RID18080
| RID18080
|
|
|-
| int28
| 28
| unsegmented region of left hypothalamus
| rgb(165,42,42)
| RID6639
| RID6639
| CCAX-RID6639-L-U
|
|-
| int31
| 31
| choroid plexus of left cerebral hemisphere
| rgb(88,106,215)
| RID27793
| RID27793
|
|
|-
| int34
| 34
| left superior cerebellar peduncle
| rgb(122,135,50)
| RID18078
| RID18078
|
|
|-
| int35
| 35
| unsegmented region of pons
| rgb(51,50,135)
| RID6728
| RID6728
| CCAX-RID6728-U
|
|-
| int40
| 40
| unsegmented region of midbrain
| rgb(205,62,78)
| RID6768
| RID6768
| CCAX-RID6768-U
|
|-
| int41
| 41
| white matter of right cerebral hemisphere
| rgb(0,225,0)
| RID16997
| RID16997
|
|
|-
| int43
| 43
| right lateral ventricle
| rgb(88,106,215)
| RID13806
| RID13806
|
|
|-
| int44
| 44
| temporal horn of right lateral ventricle
| rgb(88,106,215)
| RID13802
| RID13802
|
|
|-
| int46
| 46
| white matter of right hemisphere of cerebellum
| rgb(220,248,164)
| RID17312
| RID17312
|
|
|-
| int47
| 47
| right cerebellar cortex
| rgb(230,148,34)
| RID15573
| RID15573
|
|
|-
| int49
| 49
| right thalamus
| rgb(0,118,14)
| RID13495
| RID13495
|
|
|-
| int50
| 50
| right caudate nucleus
| rgb(122,186,220)
| RID21019
| RID21019
|
|
|-
| int51
| 51
| right putamen
| rgb(236,13,176)
| RID21014
| RID21014
|
|
|-
| int52
| 52
| right globus pallidus pars externa
| rgb(13,48,255)
| RID18434
| RID18434
|
|
|-
| int53
| 53
| right hippocampus
| rgb(220,216,20)
| RID26564
| RID26564
|
|
|-
| int54
| 54
| right amygdala
| rgb(103,255,255)
| RID15699
| RID15699
|
|
|-
| int58
| 58
| right nucleus accumbens
| rgb(255,165,0)
| RID21021
| RID21021
|
|
|-
| int60
| 60
| unsegmented region of right hypothalamus
| rgb(165,42,42)
| RID6639
| RID6639
| CCAX-RID6639-R-U
|
|-
| int61
| 61
| medulla oblongata
| rgb(135,206,235)
| RID6681
| RID6681
|
|
|-
| int63
| 63
|choroid plexus of right cerebral hemisphere
| rgb(88,106,215)
| RID27792
| RID27792
|
|
|-
| int66
| 66
| left substantia nigra
| rgb(122,135,50)
| RID20742
| RID20742
|
|
|-
| int71
| 71
| right substantia nigra
| rgb(122,135,50)
| RID20741
| RID20741
|
|
|-
| int72
| 72
| pineal body
| rgb(120,190,150)
| RID6576
| RID6576
|
|
|-
| int78
| 78
| left optic tract
| rgb(255,148,10)
| RID22698
| RID22698
|
|
|-
| int79
| 79
| left red nucleus
| rgb(255,148,10)
| RID20702
| RID20702
|
|
|-
| int83
| 83
| right globus pallidus pars interna
| rgb(13,48,255)
| RID18437
| RID18437
|
|
|-
| int84
| 84
| right red nucleus
| rgb(255,218,185)
| RID20701
| RID20701
|
|
|-
| int85
| 85
| optic chiasm
| rgb(234,169,30)
| RID6641
| RID6641
|
|
|-
| int96
| 96
| pellucid septum
| rgb(205,10,125)
| RID6525
| RID6525
|
|
|-
| int100
| 100
| left mammillothalamic tract
| rgb(124,140,178)
| RID17575
| RID17575
| CCAX-RID17563-L
|
|-
| int142
| 142
| anterior commissure
| rgb(221,226,68)
| RID6911
| RID6911
|
|
|-
| int200
| 200
| right mammillothalamic tract
| rgb(0,50,128)
| RID17574
| RID17574
| CCAX-RID17563-R
|
|-
| int216
| 216
| right optic tract
| rgb(255,204,102)
| RID22697
| RID22697
|
|
|-
| int1000
| 1000
| unsegmented region of left insula
| rgb(125,5,25)
| RID13871
| RID13871
| CCAX-RID13871-U
|
|-
| int1001
| 1001
| left superior temporal gyrus (banks of left superior temporal sulcus)
| rgb(25,100,40)
| RID20309
| RID13889
|
|
|-
| int1002
| 1002
| caudal part of left anterior cingulate gyrus
| rgb(125,100,160)
| RID26841
| RID26841
| CCAX-RID26841-S
|
|-
| int1003
| 1003
| posterior part of left middle frontal gyrus
| rgb(100,25,0)
| RID26835
| RID14075
|
|
|-
| int1005
| 1005
| left cuneus
| rgb(220,20,100)
| RID20356
| RID26552
|
|
|-
| int1006
| 1006
| left ambiens gyrus
| rgb(220,20,10)
| RID26595
| RID26595
|
|
|-
| int1007
| 1007
| left fusiform gyrus
| rgb(180,220,140)
| RID26541
| RID26541
|
|
|-
| int1008
| 1008
| unsegmented region of left inferior parietal lobule
| rgb(220,60,220)
| RID27590
| RID14108
| CCAX-RID14108-U
|
|-
| int1009
| 1009
| left inferior temporal gyrus
| rgb(180,40,120)
| RID20315
| RID13893
|
|
|-
| int1010
| 1010
| isthmus of left cingulate gyrus
| rgb(140,20,140)
| RID20384
| RID14043
|
|
|-
| int1011
| 1011
| left lateral occipital gyrus
| rgb(20,30,140)
| RID20353
| RID13938
|
|
|-
| int1012
| 1012
| left lateral orbital gyrus
| rgb(35,75,50)
| RID20293
| RID13924
|
|
|-
| int1013
| 1013
| left lingual gyrus
| rgb(225,140,140)
| RID20359
| RID26554
|
|
|-
| int1014
| 1014
| left straight gyrus
| rgb(200,35,75)
| RID20278
| RID13906
|
|
|-
| int1015
| 1015
| left middle temporal gyrus
| rgb(160,100,50)
| RID20312
| RID13891
|
|
|-
| int1016
| 1016
| left parahippocampal gyrus
| rgb(252,252,252)
| RID20306
| RID13956
|
|
|-
| int1017
| 1017
| left paracentral lobule
| rgb(20,220,60)
| RID27593
| RID14112
|
|
|-
| int1018
| 1018
| opercular part of left inferior frontal gyrus
| rgb(60,220,60)
| RID22705
| RID13978
|
|
|-
| int1019
| 1019
| orbital part of left inferior frontal gyrus
| rgb(220,180,140)
| RID22708
| RID13981
|
|
|-
| int1020
| 1020
| triangular part of left inferior frontal gyrus
| rgb(220,60,20)
| RID22702
| RID13975
|
|
|-
| int1021
| 1021
| left visual cortex
| rgb(120,100,60)
| RID25841
| RID25841
|
|
|-
| int1022
| 1022
| left postcentral gyrus
| rgb(220,20,20)
| RID20334
| RID13928
|
|
|-
| int1023
| 1023
| left posterior cingulate gyrus
| rgb(220,180,220)
| RID20378
| RID14049
|
|
|-
| int1024
| 1024
| left precentral gyrus
| rgb(60,20,220)
| RID20275
| RID13912
|
|
|-
| int1025
| 1025
| left precuneus
| rgb(160,140,180)
| RID20346
| RID13963
|
|
|-
| int1026
| 1026
| rostral part of left anterior cingulate gyrus
| rgb(80,20,140)
| RID26838
| RID26838
| CCAX-RID26838-S
| look at structure id
|-
| int1027
| 1027
| anterior part of left middle frontal gyrus
| rgb(75,50,125)
| RID26832
| RID14069
|
|
|-
| int1028
| 1028
| left superior frontal gyrus
| rgb(20,220,160)
| RID20269
| RID13903
|
|
|-
| int1029
| 1029
| left superior parietal lobule
| rgb(20,180,140)
| RID20343
| RID14110
|
| may include precuneus in labeling
|-
| int1030
| 1030
| left superior temporal gyrus
| rgb(140,220,220)
| RID20309
| RID13889
|
|
|-
| int1031
| 1031
| left supramarginal gyrus
| rgb(80,160,20)
| RID20337
| RID13930
|
| May include angular gyrus
|-
| int1032
| 1032
| left frontal pole
| rgb(100,0,100)
| RID26767
| RID20409
|
|
|-
| int1033
| 1033
| left temporal pole
| rgb(70,70,70)
| RID26770
| RID20416
|
|
|-
| int1034
| 1034
| left transverse temporal gyrus
| rgb(150,150,200)
| RID20330
| RID26543
|
|
|-
| int2000
| 2000
| unsegmented region of right insula
| rgb(80,196,98)
| RID13870
| RID13870
| CCAX-RID13870-U
|
|-
| int2001
| 2001
| right superior temporal gyrus (banks of right superior temporal sulcus)
| rgb(25,100,40)
| RID20308
| RID13888
|
|
|-
| int2002
| 2002
| caudal part of right anterior cingulate gyrus
| rgb(125,100,160)
| RID26840
| RID26840
| CCAX-RID26840-S
|
|-
| int2003
| 2003
| posterior part of right middle frontal gyrus
| rgb(100,25,0)
| RID26834
| RID14074
|
|
|-
| int2005
| 2005
| right cuneus
| rgb(220,20,100)
| RID20355
| RID26551
|
|
|-
| int2006
| 2006
| right ambiens gyrus
| rgb(220,20,100)
| RID26594
| RID26594
|
|
|-
| int2007
| 2007
| right fusiform gyrus
| rgb(180,220,140)
| RID20317
| RID26540
|
|
|-
| int2008
| 2008
| unsegmented region of right inferior parietal lobule
| rgb(220,60,220)
| RID15673
| RID14107
| CCAX-RID14107-U
|
|-
| int2009
| 2009
| right inferior temporal gyrus
| rgb(180,40,120)
| RID20314
| RID13892
|
|
|-
| int2010
| 2010
| isthmus of right cingulate gyrus
| rgb(140,20,140)
| RID20383
| RID14042
|
|
|-
| int2011
| 2011
| right lateral occipital gyrus
| rgb(20,30,140)
| RID20352
| RID13937
|
|
|-
| int2012
| 2012
| right lateral orbital gyrus
| rgb(35,75,50)
| RID20292
| RID13923
|
|
|-
| int2013
| 2013
| right lingual gyrus
| rgb(225,140,140)
| RID20358
| RID26553
|
|
|-
| int2014
| 2014
| right straight gyrus
| rgb(200,35,75)
| RID20277
| RID13905
|
|
|-
| int2015
| 2015
| right middle temporal gyrus
| rgb(160,100,50)
| RID20311
| RID13890
|
|
|-
| int2016
| 2016
| right parahippocampal gyrus
| rgb(20,220,60)
| RID20305
| RID13955
|
|
|-
| int2017
| 2017
| right paracentral lobule
| rgb(60,220,60)
| RID27592
| RID14111
|
|
|-
| int2018
| 2018
| opercular part of right inferior frontal gyrus
| rgb(220,180,140)
| RID22704
| RID13977
|
|
|-
| int2019
| 2019
| orbital part of right inferior frontal gyrus
| rgb(20,100,50)
| RID22707
| RID13980
|
|
|-
| int2020
| 2020
| triangular part of right inferior frontal gyrus
| rgb(220,60,20)
| RID22701
| RID13974
|
|
|-
| int2021
| 2021
| right visual cortex
| rgb(120,100,60)
| RID25840
| RID25840
|
|
|-
| int2022
| 2022
| right postcentral gyrus
| rgb(220,20,20)
| RID20333
| RID13927
|
|
|-
| int2023
| 2023
| right posterior cingulate gyrus
| rgb(220,180,220)
| RID20377
| RID14048
|
|
|-
| int2024
| 2024
| right precentral gyrus
| rgb(60,20,220)
| RID20274
| RID13911
|
|
|-
| int2025
| 2025
| right precuneus
| rgb(160,140,180)
| RID20345
| RID13962
|
|
|-
| int2026
| 2026
| rostral part of right anterior cingulate gyrus
| rgb(80,20,140)
| RID26837
| RID26837
| CCAX-RID26837-S
| look at structure id
|-
| int2027
| 2027
| anterior part of right middle frontal gyrus
| rgb(75,50,125)
| RID26831
| RID14068
|
|
|-
| int2028
| 2028
| right superior frontal gyrus
| rgb(20,220,160)
| RID20268
| RID13902
|
|
|-
| int2029
| 2029
| right superior parietal lobule
| rgb(20,180,140)
| RID20342
| RID14109
|
| may include precuneus
|-
| int2030
| 2030
| right superior temporal gyrus
| rgb(140,220,220)
| RID20308
| RID13888
|
|
|-
| int2031
| 2031
| right supramarginal gyrus
| rgb(80,160,20)
| RID20336
| RID13929
|
| may include angular gyrus
|-
| int2032
| 2032
| right frontal pole
| rgb(100,0,100)
| RID26766
| RID20408
|
|
|-
| int2033
| 2033
| right temporal pole
| rgb(70,70,70)
| RID26769
| RID20415
|
|
|-
| int2034
| 2034
| right transverse temporal gyrus
| rgb(150,150,200)
| RID20329
| RID26542
|
|
|-
| int2108
| 2108
| right angular and supramarginal gyri (obsolete label)
| rgb(230,250,230)
| RID22701
| RID13974
|
|
|-
| int3000
| 3000
| right claustrum
| rgb(230,250,230)
| RID15701
| RID15701
|
|
|-
| int3001
| 3001
| left claustrum
| rgb(230,155,215)
| RID15700
| RID15700
|
|
|-
| int3002
| 3002
| right mammillary body
| rgb(130,155,95)
| RID26776
| RID26776
|
|
|-
| int3003
| 3003
| left mammillary body
| rgb(155,230,255)
| RID26777
| RID26777
|
|
|-
| int3004
| 3004
| corpus callosum
| rgb(250,240,20)
| RID6915
| RID6915
|
|
|-
| int3005
| 3005
| right fornix of forebrain
| rgb(35,235,155)
| RID18106
| RID18106
|
|
|-
| int3007
| 3007
| left fornix of forebrain
| rgb(75,35,115)
| RID18107
| RID18107
|
|
|-
| int3008
| 3008
| infundibulum of neurohypophysis
| rgb(35,195,35)
| RID15529
| RID15529
|
|
|-
| int3011
| 3011
| adenohypophysis
| rgb(235,225,115)
| RID15522
| RID15522
|
|
|-
| int3012
| 3012
| unsegmented region of neurohypophysis
| rgb(220,180,205)
| RID6645
| RID6645
| CCAX-RID6645-U
|
|}

=== Thalamic Nuclei Expansion ===
{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
! radlex_id
! radlex_structure_id
|-
| 500
| right internal medullary lamina
| rgb(200,200,200)
| style="background:#C8C8C8"|
| RID18025
| RID18025
|-
| 501
| left internal medullary lamina
| rgb(200,200,200)
| style="background:#C8C8C8"|
| RID18026
| RID18026
|-
| 502
| right medial geniculate body
| rgb(125,250,21)
| style="background:#7DFA15"|
| RID20560
| RID20560
|-
| 503
| left medial geniculate body
| rgb(125,250, 21)
| style="background:#7DFA15"|
| RID20561
| RID20561
|-
| 504
| right lateral geniculate body
| rgb(102,178,255)
| style="background:#66B2FF"|
| RID20562
| RID20562
|-
| 505
| left lateral geniculate body
| rgb(102,178,255)
| style="background:#66B2FF"|
| RID20563
| RID20563
|-
| 506
| right pulvinar
| rgb(63,104,224)
| style="background:#3F68E0"|
| RID20564
| RID20564
|-
| 507
| left pulvinar
| rgb(63,104,224)
| style="background:#3F68E0"|
| RID20565
| RID20565
|-
| 508
| right anterior thalamic nucleus
| rgb(255,25,127)
| style="background:#FF197F; color:#fff"|in the old SPL-BrainAtlas-Colorfile.txt ''L'' and ''R'' are mislabeled (switched)
| RID20544
| RID20544
|-
| 509
| left anterior thalamic nucleus
| rgb(255,25,127)
| style="background:#FF197F; color:#fff"|in the old SPL-BrainAtlas-Colorfile.txt ''L'' and ''R'' are mislabeled (switched)
| RID20545
| RID20545
|-
| 510
| right dorsomedial thalamic nucleus
| rgb(60,189,130)
| style="background:#3CBD82"|
| RID20535
| RID20535
|-
| 511
| left dorsomedial thalamic nucleus
| rgb(60,189,130)
| style="background:#3CBD82"|
| RID20536
| RID20536
|-
| 512
| right centromedian thalamic nucleus
| rgb(188,181,105)
| style="background:#BCB569"|
| RID20568
| RID20568
|-
| 513
| left centromedian thalamic nucleus
| rgb(188,181,105)
| style="background:#BCB569"|
| RID20569
| RID20569
|-
| 514
| right ventral anterior thalamic nucleus
| rgb(254,213,0)
| style="background:#FED500"|
| RID20929
| RID20929
|-
| 515
| left ventral anterior thalamic nucleus
| rgb(254,213,0)
| style="background:#FED500"|
| RID20930
| RID20930
|-
| 516
| right ventral lateral thalamic nucleus
| rgb(60,180,180)
| style="background:#3CB4B4"|
| RID20931
| RID20931
|-
| 517
| left ventral lateral thalamic nucleus
| rgb(60,180,180)
| style="background:#3CB4B4"|
| RID20932
| RID20932
|-
| 518
| right lateral posterior thalamic nucleus
| rgb(204,127,0)
| style="background:#CC7F00"|
| RID20927
| RID20927
|-
| 519
| left lateral posterior thalamic nucleus
| rgb(204,127,0)
| style="background:#CC7F00"|
| RID20928
| RID20928
|-
| 520
| right lateral dorsal thalamic nucleus
| rgb(175,194,221)
| style="background:#AFC2DD"|
| RID20925
| RID20925
|-
| 521
| left lateral dorsal thalamic nucleus
| rgb(175,194,221)
| style="background:#AFC2DD"|
| RID20926
| RID20926
|-
| 522
| right ventral posteromedial thalamic nucleus
| rgb(225,167,104)
| style="background:#FFA768"|
| RID20506
| RID20506
|-
| 523
| left ventral posteromedial thalamic nucleus
| rgb(225,167,104)
| style="background:#FFA768"|
| RID20507
| RID20507
|-
| 524
| right ventral posterolateral thalamic nucleus
| rgb(229,127,127)
| style="background:#E57F7F"|
| RID20504
| RID20504
|-
| 525
| left ventral posterolateral thalamic nucleus
| rgb(229,127,127)
| style="background:#E57F7F"|
| RID20505
| RID20505
|}

=== Extra Freesurfer labels ===

See [[Slicer3:Freesurfer_labels]].