View source for CCA:AtlasTools:LabelPage:Sample

__NOTOC__
[[Category:LabelPage]]
[[Category:LabelPageSlicerColorFile]]
== Title ==
'''NAC CCA Core 2010 MRI Brain Atlas'''
== Description ==
This file contains the label information that corresponds to the 2010 SPL Brain Atlas.
== Credits ==
; Author
: Ion-Florin Talos MD
: Michael Halle PhD

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

; Grants
: National Institutes of Health (NIH)'s National Center for Research Resources (NCRR),  NIH P41 RR13218.

; Creation Date
: 02/16/2009

==  Imports ==
Links to other labeltag pages go here.  The contents of those pages are imported before the data described on this page.

* [[CCA:AtlasTools:LabelPage:SampleExternal | external sample lut]]
* [[CCA:AtlasTools:LabelPage:SampleExternal2 | external sample lut (2)]]

== Lookup table information ==

These tables are just mediawiki tables with a couple of css classes included to make them sortable and declare them as Label Pages.

Generally, the workflow for Label Pages is to import an initial (and possibly large) table using a bulk data converter (say, from a CSV file), 
then make small edits through the wiki.  The label tables can be broken up into smaller tables to make it easier to browse and edit them.

=== Atlas lookup table ===

{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
| 2
| white matter of left cerebral hemisphere
| rgb(245,245,245)
| style="background:#F5F5F5"|
|-
| 4
| left lateral ventricle
| rgb(120,18,134)
| style="background:#781286"| 
|-
| 5
| temporal horn of left lateral ventricle
| rgb(196,58,250)
| style="background:#C43AFA"|
|-
| 7
| white matter of cerebellum left
| rgb(221,248,164)
| 
|-
| 8
| left cerebellar cortex
| rgb(230,148,34)
| 
|-
| 10
| left thalamus
| rgb(0,118,14)
| 
|-
| 11
| left caudate nucleus
| rgb(122,186,220)
| 
|-
| 12
| left putamen
| rgb(236,13,176)
| 
|-
| 13
| left globus pallidus pars externa
| rgb(12,48,255)
| 
|-
| 14
| wall of third ventricle
| rgb(204,182,142)
| 
|-
| 15
| fourth ventricle
| rgb(42,204,164)
| 
|-
| 17
| left hippocampus
| rgb(220,216,20)
| 
|-
| 18
| left amygdala
| rgb(103,255,255)
| 
|-
| 24
| third ventricle (1)
| rgb(60,60,60)
| 
|-
| 25
| left globus pallidus pars interna
| rgb(255,165,0)
| 
|-
| 26
| left nucleus accumbens
| rgb(165,0,255)
| 
|-
| 27
| left middle cerebellar peduncle
| rgb(0,255,127)
| 
|-
| 28
| left hypothalamus
| rgb(165,42,42)
| 
|-
| 34
| left superior cerebellar peduncle
| rgb(122,135,50)
| 
|-
| 35
| pons
| rgb(51,50,135)
| 
|-
| 40
| midbrain
| rgb(205,62,78)
| 
|-
| 41
| white matter of right cerebral hemisphere
| rgb(0,225,0)
| 
|-
| 43
| right lateral ventricle
| rgb(120,18,134)
| 
|-
| 44
| temporal horn of right lateral ventricle
| rgb(196,58,250)
| 
|-
| 46
| white matter of cerebellum right
| rgb(220,248,164)
| 
|-
| 47
| right cerebellar cortex
| rgb(230,148,34)
| 
|-
| 49
| right thalamus
| rgb(0,118,14)
| 
|-
| 50
| right caudate nucleus
| rgb(122,186,220)
| 
|-
| 51
| right putamen
| rgb(236,13,176)
| 
|-
| 52
| right globus pallidus pars externa
| rgb(13,48,255)
| 
|-
| 53
| right hippocampus
| rgb(220,216,20)
| 
|-
| 54
| right amygdala
| rgb(103,255,255)
| 
|-
| 55
| right insula
| rgb(80,196,98)
| 
|-
| 58
| right nucleus accumbens
| rgb(255,165,0)
| 
|-
| 60
| right hypothalamus
| rgb(165,42,42)
| 
|-
| 61
| medulla oblongata
| rgb(135,206,235)
| 
|-
| 63
| choroid plexus of right lateral ventricle
| rgb(0,200,221)
| 
|-
| 66
| left substantia nigra
| rgb(122,135,50)
| 
|-
| 71
| right substantia nigra
| rgb(122,135,50)
| 
|-
| 72
| pineal body
| rgb(120,190,150)
| 
|-
| 78
| left optic tract
| rgb(255,148,10)
| 
|-
| 79
| left red nucleus
| rgb(255,148,10)
| 
|-
| 84
| right red nucleus
| rgb(255,218,185)
| 
|-
| 85
| optic chiasm
| rgb(234,169,30)
| 
|-
| 96
| pellucid septum
| rgb(205,10,125)
| 
|-
| 100
| left mammillothalamic tract
| rgb(124,140,178)
| 
|-
| 142
| anterior commissure
| rgb(221,226,68)
| 
|-
| 200
| right mammillothalamic tract
| rgb(0,50,128)
| 
|-
| 216
| right optic tract
| rgb(255,204,102)
| 
|-
| 1000
| left insula
| rgb(25,5,25)
| 
|-
| 1001
| left superior temporal gyrus (1)
| rgb(25,100,40)
| 
|-
| 1002
| left cingulate gyrus (1)
| rgb(125,100,160)
| 
|-
| 1003
| left middle frontal gyrus (1)
| rgb(100,25,0)
| 
|-
| 1005
| left cuneus
| rgb(220,20,100)
| 
|-
| 1006
| left ambiens gyrus
| rgb(220,20,10)
| 
|-
| 1007
| left fusiform gyrus
| rgb(180,220,140)
| 
|-
| 1008
| left inferior parietal lobule
| rgb(220,60,220)
| 
|-
| 1009
| left inferior temporal gyrus
| rgb(180,40,120)
| 
|-
| 1010
| left cingulate gyrus (2)
| rgb(140,20,140)
| 
|-
| 1011
| left lateral occipital gyrus
| rgb(20,30,140)
| 
|-
| 1012
| left orbital gyri
| rgb(35,75,50)
| 
|-
| 1013
| left lingual gyrus
| rgb(225,140,140)
| 
|-
| 1014
| left straight gyrus
| rgb(200,35,75)
| 
|-
| 1015
| left middle temporal gyrus
| rgb(160,100,50)
| 
|-
| 1017
| left paracentral lobule
| rgb(20,220,60)
| 
|-
| 1018
| opercular part of left inferior frontal gyrus
| rgb(60,220,60)
| 
|-
| 1019
| orbital part of left inferior frontal gyrus
| rgb(220,180,140)
| 
|-
| 1020
| triangular part of left inferior frontal gyrus
| rgb(220,60,20)
| 
|-
| 1021
| left visual cortex
| rgb(120,100,60)
| 
|-
| 1022
| left postcentral gyrus
| rgb(220,20,20)
| 
|-
| 1023
| left cingulate gyrus (1)
| rgb(220,180,220)
| 
|-
| 1024
| left precentral gyrus
| rgb(60,20,220)
| 
|-
| 1025
| left precuneus
| rgb(160,140,180)
| 
|-
| 1026
| left cingulate gyrus (3)
| rgb(80,20,140)
| 
|-
| 1027
| left middle frontal gyrus (2)
| rgb(75,50,125)
| 
|-
| 1028
| left superior frontal gyrus (1)
| rgb(20,220,160)
| 
|-
| 1029
| left superior parietal lobule and precuneus
| rgb(20,180,140)
| 
|-
| 1030
| left superior temporal gyrus
| rgb(140,220,220)
| 
|-
| 1031
| left angular and supramarginal gyrus
| rgb(80,160,20)
| 
|-
| 1032
| left frontal pole
| rgb(100,0,100)
| 
|-
| 1033
| left temporal pole
| rgb(70,70,70)
| 
|-
| 1034
| left transverse temporal gyri
| rgb(150,150,200)
| 
|-
| 2001
| right superior temporal gyrus (2)
| rgb(25,100,40)
| 
|-
| 2003
| right middle frontal gyrus (1)
| rgb(100,25,0)
| 
|-
| 2005
| right cuneus
| rgb(220,20,100)
| 
|-
| 2006
| right parahippocampal gyrus
| rgb(220,20,10)
| 
|-
| 2007
| right fusiform gyrus
| rgb(180,220,140)
| 
|-
| 2008
| right angular and supramarginal gyri
| rgb(220,60,220)
| 
|-
| 2009
| right inferior temporal gyrus
| rgb(180,40,120)
| 
|-
| 2010
| right cingulate gyrus (2)
| rgb(140,20,140)
| 
|-
| 2011
| right lateral occipital gyrus
| rgb(20,30,140)
| 
|-
| 2012
| right orbital gyri (1)
| rgb(35,75,50)
| 
|-
| 2013
| right lingual gyrus
| rgb(225,140,140)
| 
|-
| 2014
| right straight gyrus
| rgb(200,35,75)
| 
|-
| 2015
| right middle temporal gyrus
| rgb(160,100,50)
| 
|-
| 2017
| right paracentral lobule
| rgb(60,220,60)
| 
|-
| 2018
| opercular part of right inferior frontal gyrus
| rgb(220,180,140)
| 
|-
| 2019
| orbital part of right inferior frontal gyrus
| rgb(20,100,50)
| 
|-
| 2020
| triangular part of right inferior frontal gyrus
| rgb(220,60,20)
| 
|-
| 2021
| right visual cortex
| rgb(120,100,60)
| 
|-
| 2022
| right postcentral gyrus
| rgb(220,20,20)
| 
|-
| 2023
| right cingulate gyrus (1)
| rgb(220,180,220)
| 
|-
| 2024
| right precentral gyrus
| rgb(60,20,220)
| 
|-
| 2025
| right precuneus
| rgb(160,140,180)
| 
|-
| 2027
| right middle frontal gyrus (1)
| rgb(75,50,125)
| 
|-
| 2028
| right superior frontal gyrus
| rgb(20,220,160)
| 
|-
| 2029
| right superior parietal lobule
| rgb(20,180,140)
| 
|-
| 2030
| right superior temporal gyrus (3)
| rgb(140,220,220)
| 
|-
| 2031
| right supramarginal gyrus
| rgb(80,160,20)
| 
|-
| 2032
| right frontal pole
| rgb(100,0,100)
| 
|-
| 2033
| right temporal pole
| rgb(70,70,70)
| 
|-
| 2108
| right angular and supramarginal gyri
| rgb(230,250,230)
| 
|-
| 3000
| right claustrum
| rgb(230,250,230)
| 
|-
| 3001
| left claustrum
| rgb(230,155,215)
| 
|-
| 3002
| right mamillary body
| rgb(130,155,95)
| 
|-
| 3003
| left mamillary body
| rgb(155,230,255)
| 
|-
| 3004
| corpus callosum
| rgb(135,185,205)
| 
|-
| 3005
| right fornix of forebrain
| rgb(35,235,155)
| 
|-
| 3007
| left fornix of forebrain
| rgb(75,35,115)
| 
|-
| 3008
| infundibulum of neurohypophysis
| rgb(35,195,35)
| 
|-
| 3011
| adenohypophysis
| rgb(235,225,115)
| 
|-
| 3012
| neurohypophysis
| rgb(220,180,205)
| 
|-
|}

=== Thalamic Nuclei Expansion ===
{| class="wikitable sortable labelpage labelpagetable" border="1"
! integer_label
! text_label
! color
! notes
|-
| 500
| internal medullar lamina R
| rgb(200,200,200)
|  style="background:#C8C8C8"|
|-
| 501
| internal medullar lamina L
| rgb(200,200,200)
| style="background:#C8C8C8"|
|-
| 502
| medial geniculate body R
| rgb(125,250,21)
| style="background:#7DFA15"|
|-
| 503
| medial geniculate body L
| rgb(125,250, 21)
| style="background:#7DFA15"|
|-
| 504
| lateral geniculate body R
| rgb(102,178,255)
| style="background:#66B2FF"|
|-
| 505
| lateral geniculate body L
| rgb(102,178,255)
| style="background:#66B2FF"|
|-
| 506
| pulvinar R
| rgb(63,104,224)
| style="background:#3F68E0"|
|-
| 507
| pulvinar L
| rgb(63,104,224)
| style="background:#3F68E0"|
|-
| 508
| anterior thalamic nucleus R
| rgb(255,25,127)
| style="background:#FF197F"|in the old SPL-BrainAtlas-Colorfile.txt ''L'' and ''R'' are mislabeled (switched)
|-
| 509
| anterior thalamic nucleus L
| rgb(255,25,127)
| style="background:#FF197F"|in the old SPL-BrainAtlas-Colorfile.txt ''L'' and ''R'' are mislabeled (switched)
|-
| 510
| dorsomedial thalamic nucleus R
| rgb(60,189,130)
| style="background:#3CBD82"|
|-
| 511
| dorsomedial thalamic nucleus L
| rgb(60,189,130)
| style="background:#3CBD82"|
|-
| 512
| centromedian thalamic nucleus R
| rgb(188,181,105)
| style="background:#BCB569"|
|-
| 513
| centromedian thalamic nucleus L
| rgb(188,181,105)
| style="background:#BCB569"|
|-
| 514
| ventral anterior thalamic nucleus R
| rgb(254,213,0)
| style="background:#FED500"|
|-
| 515
| ventral anterior thalamic nucleus R
| rgb(254,213,0)
| style="background:#FED500"|
|-
| 516
| ventral lateral thalamic nucleus R
| rgb(60,180,180)
| style="background:#3CB4B4"|
|-
| 517
| ventral lateral thalamic nucleus L
| rgb(60,180,180)
| style="background:#3CB4B4"|
|-
| 518
| lateral posterior thalamic nucleus R
| rgb(204,127,0)
| style="background:#CC7F00"|
|-
| 519
| lateral posterior thalamic nucleus L
| rgb(204,127,0)
| style="background:#CC7F00"|
|-
| 520
| lateral dorsal thalamic nucleus R
| rgb(175,194,221)
| style="background:#AFC2DD"|
|-
| 521
| lateral dorsal thalamic nucleus L
| rgb(175,194,221)
| style="background:#AFC2DD"|
|-
| 522
| VPM thalamic nucleus R
| rgb(225,167,104)
| style="background:#FFA768"|
|-
| 523
| VPM thalamic nucleus L
| rgb(225,167,104)
| style="background:#FFA768"|
|-
| 524
| VPL thalamic nucleus R
| rgb(229,127,127)
| style="background:#E57F7F"|
|-
| 525
| VPL thalamic nucleus L
| rgb(229,127,127)
| style="background:#E57F7F"|
|}

===Small addon table===
{| class="wikitable sortable labelpage labelpagetable" border="1"
|+ style="font-size: 1em; font-style: bold; background:white" | user interface colors
! integer_label
! text_label
! color
! notes
|-
| 0
| background
| rgb(0,0,0)
| The background value is stored here because it isn't anatomical.
|}

== Output color file ==
An external script processes this page and produces the following color file, suitable for Slicer.

Pages suitable for generating Slicer color files should be marked with the Category "LabelPageSlicerColorFile".

TODO: Generate this file automatically as part of wiki editing.