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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 >