Dear Thao,
Below is a list of the numbers, label names and colour
information used in the MGH colourmaps. I think this
should give you the information that you require (plus
quite a few labels which are not present in the atlases).
This comes from a lookup table provided with FreeSurfer.
We provide the same colourmaps as MGH-Subcortical
and MGH-Cortical.
I hope this helps.
All the best,
Mark
#No. Label Name: R G B A
0 Unknown 0 0 0 0
1 Left-Cerebral-Exterior 70 130 180 0
2 Left-Cerebral-White-Matter 245 245 245 0
3 Left-Cerebral-Cortex 205 62 78 0
4 Left-Lateral-Ventricle 120 18 134 0
5 Left-Inf-Lat-Vent 196 58 250 0
6 Left-Cerebellum-Exterior 0 148 0 0
7 Left-Cerebellum-White-Matter 220 248 164 0
8 Left-Cerebellum-Cortex 230 148 34 0
9 Left-Thalamus 0 118 14 0
10 Left-Thalamus-Proper 0 118 14 0
11 Left-Caudate 122 186 220 0
12 Left-Putamen 236 13 176 0
13 Left-Pallidum 12 48 255 0
14 3rd-Ventricle 204 182 142 0
15 4th-Ventricle 42 204 164 0
16 Brain-Stem 119 159 176 0
17 Left-Hippocampus 220 216 20 0
18 Left-Amygdala 103 255 255 0
19 Left-Insula 80 196 98 0
20 Left-Operculum 60 58 210 0
21 Line-1 60 58 210 0
22 Line-2 60 58 210 0
23 Line-3 60 58 210 0
24 CSF 60 60 60 0
25 Left-Lesion 255 165 0 0
26 Left-Accumbens-area 255 165 0 0
27 Left-Substancia-Nigra 0 255 127 0
28 Left-VentralDC 165 42 42 0
29 Left-undetermined 135 206 235 0
30 Left-vessel 160 32 240 0
31 Left-choroid-plexus 0 200 200 0
32 Left-F3orb 100 50 100 0
33 Left-lOg 135 50 74 0
34 Left-aOg 122 135 50 0
35 Left-mOg 51 50 135 0
36 Left-pOg 74 155 60 0
37 Left-Stellate 120 62 43 0
38 Left-Porg 74 155 60 0
39 Left-Aorg 122 135 50 0
40 Right-Cerebral-Exterior 70 130 180 0
41 Right-Cerebral-White-Matter 0 225 0 0
42 Right-Cerebral-Cortex 205 62 78 0
43 Right-Lateral-Ventricle 120 18 134 0
44 Right-Inf-Lat-Vent 196 58 250 0
45 Right-Cerebellum-Exterior 0 148 0 0
46 Right-Cerebellum-White-Matter 220 248 164 0
47 Right-Cerebellum-Cortex 230 148 34 0
48 Right-Thalamus 0 118 14 0
49 Right-Thalamus-Proper 0 118 14 0
50 Right-Caudate 122 186 220 0
51 Right-Putamen 236 13 176 0
52 Right-Pallidum 13 48 255 0
53 Right-Hippocampus 220 216 20 0
54 Right-Amygdala 103 255 255 0
55 Right-Insula 80 196 98 0
56 Right-Operculum 60 58 210 0
57 Right-Lesion 255 165 0 0
58 Right-Accumbens-area 255 165 0 0
59 Right-Substancia-Nigra 0 255 127 0
60 Right-VentralDC 165 42 42 0
61 Right-undetermined 135 206 235 0
62 Right-vessel 160 32 240 0
63 Right-choroid-plexus 0 200 221 0
64 Right-F3orb 100 50 100 0
65 Right-lOg 135 50 74 0
66 Right-aOg 122 135 50 0
67 Right-mOg 51 50 135 0
68 Right-pOg 74 155 60 0
69 Right-Stellate 120 62 43 0
70 Right-Porg 74 155 60 0
71 Right-Aorg 122 135 50 0
72 5th-Ventricle 120 190 150 0
73 Left-Interior 122 135 50 0
74 Right-Interior 122 135 50 0
75 Left-Lateral-Ventricles 120 18 134 0
76 Right-Lateral-Ventricles 120 18 134 0
77 WM-hypointensities 200 70 255 0
78 Left-WM-hypointensities 255 148 10 0
79 Right-WM-hypointensities 255 148 10 0
80 non-WM-hypointensities 164 108 226 0
81 Left-non-WM-hypointensities 164 108 226 0
82 Right-non-WM-hypointensities 164 108 226 0
83 Left-F1 255 218 185 0
84 Right-F1 255 218 185 0
85 Optic-Chiasm 234 169 30 0
86 Corpus_Callosum 250 255 50 0
96 Left-Amygdala-Anterior 205 10 125 0
97 Right-Amygdala-Anterior 205 10 125 0
98 Dura 160 32 240 0
100 Left-wm-intensity-abnormality 124 140 178 0
101 Left-caudate-intensity-abnormality 125 140 178 0
102 Left-putamen-intensity-abnormality 126 140 178 0
103 Left-accumbens-intensity-abnormality 127 140 178 0
104 Left-pallidum-intensity-abnormality 124 141 178 0
105 Left-amygdala-intensity-abnormality 124 142 178 0
106 Left-hippocampus-intensity-abnormality 124 143 178 0
107 Left-thalamus-intensity-abnormality 124 144 178 0
108 Left-VDC-intensity-abnormality 124 140 179 0
109 Right-wm-intensity-abnormality 124 140 178 0
110 Right-caudate-intensity-abnormality 125 140 178 0
111 Right-putamen-intensity-abnormality 126 140 178 0
112 Right-accumbens-intensity-abnormality 127 140 178 0
113 Right-pallidum-intensity-abnormality 124 141 178 0
114 Right-amygdala-intensity-abnormality 124 142 178 0
115 Right-hippocampus-intensity-abnormality 124 143 178 0
116 Right-thalamus-intensity-abnormality 124 144 178 0
117 Right-VDC-intensity-abnormality 124 140 179 0
118 Epidermis 255 20 147 0
119 Conn-Tissue 205 179 139 0
120 SC-Fat/Muscle 238 238 209 0
121 Cranium 200 200 200 0
122 CSF-SA 74 255 74 0
123 Muscle 238 0 0 0
124 Ear 0 0 139 0
125 Adipose 173 255 47 0
126 Spinal-Cord 133 203 229 0
127 Soft-Tissue 26 237 57 0
128 Nerve 34 139 34 0
129 Bone 30 144 255 0
130 Air 147 19 173 0
131 Orbital-Fat 238 59 59 0
132 Tongue 221 39 200 0
133 Nasal-Structures 238 174 238 0
134 Globe 255 0 0 0
135 Teeth 72 61 139 0
136 Left-Caudate/Putamen 21 39 132 0
137 Right-Caudate/Putamen 21 39 132 0
138 Left-Claustrum 65 135 20 0
139 Right-Claustrum 65 135 20 0
140 Cornea 134 4 160 0
142 Diploe 221 226 68 0
143 Vitreous-Humor 255 255 254 0
144 Lens 52 209 226 0
145 Aqueous-Humor 239 160 223 0
146 Outer-Table 70 130 180 0
147 Inner-Table 70 130 181 0
148 Periosteum 139 121 94 0
149 Endosteum 224 224 224 0
150 R/C/S 255 0 0 0
151 Iris 205 205 0 0
152 SC-Adipose/Muscle 238 238 209 0
153 SC-Tissue 139 121 94 0
154 Orbital-Adipose 238 59 59 0
155 Left-IntCapsule-Ant 238 59 59 0
156 Right-IntCapsule-Ant 238 59 59 0
157 Left-IntCapsule-Pos 62 10 205 0
158 Right-IntCapsule-Pos 62 10 205 0
193 Left-hippocampal_fissure 0 196 255 0
194 Left-CADG-head 255 164 164 0
195 Left-subiculum 196 196 0 0
196 Left-fimbria 0 100 255 0
197 Right-hippocampal_fissure 128 196 164 0
198 Right-CADG-head 0 126 75 0
199 Right-subiculum 128 96 64 0
200 Right-fimbria 0 50 128 0
201 alveus 255 204 153 0
202 perforant_pathway 255 128 128 0
203 parasubiculum 255 255 0 0
204 presubiculum 64 0 64 0
205 subiculum 0 0 255 0
206 CA1 255 0 0 0
207 CA2 128 128 255 0
208 CA3 0 128 0 0
209 CA4 196 160 128 0
210 GC-DG 32 200 255 0
211 HATA 128 255 128 0
212 fimbria 204 153 204 0
213 lateral_ventricle 121 17 136 0
214 molecular_layer_HP 128 0 0 0
215 hippocampal_fissure 128 32 255 0
216 entorhinal_cortex 255 204 102 0
217 molecular_layer_subiculum 128 128 128 0
218 Amygdala 104 255 255 0
219 Cerebral_White_Matter 0 226 0 0
220 Cerebral_Cortex 205 63 78 0
221 Inf_Lat_Vent 197 58 250 0
222 Perirhinal 33 150 250 0
223 Cerebral_White_Matter_Edge 226 0 0 0
224 Background 100 100 100 0
225 Ectorhinal 197 150 250 0
250 Fornix 255 0 0 0
251 CC_Posterior 0 0 64 0
252 CC_Mid_Posterior 0 0 112 0
253 CC_Central 0 0 160 0
254 CC_Mid_Anterior 0 0 208 0
255 CC_Anterior 0 0 255 0
On 30 Nov 2009, at 17:05, Thao Do wrote:
> Hello everyone,
>
> Can anyone tell me who I should contact (maybe someone from CMA?) to
> find
> out more about how the labellings for the Harvard-Oxford
> cortical/subcortical structural atlases are obtained?
>
> Thank you kindly,
> Thao
>
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