Difference between revisions of "CCA:AtlasTools:LabelPage:Sample"

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__NOTOC__
 
__NOTOC__
−
[[Category:LabelTagPage]]
+
[[Category:LabelPage]]
 +
[[Category:LabelPageSlicerColorFile]]
 
== Title ==
 
== Title ==
 
'''NAC CCA Core 2010 MRI Brain Atlas'''
 
'''NAC CCA Core 2010 MRI Brain Atlas'''
Line 24: Line 25:
 
==  Imports ==
 
==  Imports ==
 
Links to other labeltag pages go here.  The contents of those pages are imported before the data described on this page.
 
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 ==
 
== Lookup table information ==
  
−
{| class="wikitable sortable labeltag lttable" border="1"
+
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
 
! integer_label
 
! text_label
 
! text_label
 
! color
 
! color
 
! notes
 
! notes
−
|-
 
−
| 0
 
−
| background
 
−
| rgb(0,0,0)
 
−
|
 
 
|-
 
|-
 
| 2
 
| 2
 
| white matter of left cerebral hemisphere
 
| white matter of left cerebral hemisphere
 
| rgb(245,245,245)
 
| rgb(245,245,245)
−
|  
+
| style="background:#F5F5F5"|
 
|-
 
|-
 
| 4
 
| 4
 
| left lateral ventricle
 
| left lateral ventricle
 
| rgb(120,18,134)
 
| rgb(120,18,134)
−
|  
+
| style="background:#781286"|  
 
|-
 
|-
 
| 5
 
| 5
 
| temporal horn of left lateral ventricle
 
| temporal horn of left lateral ventricle
 
| rgb(196,58,250)
 
| rgb(196,58,250)
−
|  
+
| style="background:#C43AFA"|
 
|-
 
|-
 
| 7
 
| 7
 
| white matter of cerebellum left
 
| white matter of cerebellum left
−
| rgb(220,248,164)
+
| rgb(221,248,164)
 
|  
 
|  
 
|-
 
|-
Line 649: Line 655:
 
|-
 
|-
 
|}
 
|}
 +
 +
=== 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.

Latest revision as of 15:55, 25 February 2010

Home < CCA:AtlasTools:LabelPage:Sample

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.

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

integer_label text_label color notes
2 white matter of left cerebral hemisphere rgb(245,245,245)
4 left lateral ventricle rgb(120,18,134)
5 temporal horn of left lateral ventricle rgb(196,58,250)
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

integer_label text_label color notes
500 internal medullar lamina R rgb(200,200,200)
501 internal medullar lamina L rgb(200,200,200)
502 medial geniculate body R rgb(125,250,21)
503 medial geniculate body L rgb(125,250, 21)
504 lateral geniculate body R rgb(102,178,255)
505 lateral geniculate body L rgb(102,178,255)
506 pulvinar R rgb(63,104,224)
507 pulvinar L rgb(63,104,224)
508 anterior thalamic nucleus R rgb(255,25,127) in the old SPL-BrainAtlas-Colorfile.txt L and R are mislabeled (switched)
509 anterior thalamic nucleus L rgb(255,25,127) in the old SPL-BrainAtlas-Colorfile.txt L and R are mislabeled (switched)
510 dorsomedial thalamic nucleus R rgb(60,189,130)
511 dorsomedial thalamic nucleus L rgb(60,189,130)
512 centromedian thalamic nucleus R rgb(188,181,105)
513 centromedian thalamic nucleus L rgb(188,181,105)
514 ventral anterior thalamic nucleus R rgb(254,213,0)
515 ventral anterior thalamic nucleus R rgb(254,213,0)
516 ventral lateral thalamic nucleus R rgb(60,180,180)
517 ventral lateral thalamic nucleus L rgb(60,180,180)
518 lateral posterior thalamic nucleus R rgb(204,127,0)
519 lateral posterior thalamic nucleus L rgb(204,127,0)
520 lateral dorsal thalamic nucleus R rgb(175,194,221)
521 lateral dorsal thalamic nucleus L rgb(175,194,221)
522 VPM thalamic nucleus R rgb(225,167,104)
523 VPM thalamic nucleus L rgb(225,167,104)
524 VPL thalamic nucleus R rgb(229,127,127)
525 VPL thalamic nucleus L rgb(229,127,127)

Small addon table

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.

Retrieved from "https://www.na-mic.org/w/index.php?title=CCA:AtlasTools:LabelPage:Sample&oldid=49426"