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Merge pull request #99 from cpp-lln-lab/glasser
[ENH] add glasser atlas
2 parents fa4fa8e + c6b5602 commit 582e49a

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‎.codespellrc

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[codespell]
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skip = .git,env,*build,lib
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skip = .git,env,*build,lib,*LUT.csv,*.xml
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builtin = clear,rare
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ignore-words-list = morg, fo

‎.gitignore

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# ignore virtual env
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envs/*
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# visual studio code stuff
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.vscode
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2017
atlas/visual_topography_probability_atlas/
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demos/*/derivatives
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#for testing
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coveragage_html
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lib/bids-matlab
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## MATLAB / OCTAVE gitignore template
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# From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
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# Windows default autosave extension
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*.asv
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‎.readthedocs.yml

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# Optionally set the version of Python and requirements required to build your docs
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python:
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version: 3.7
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version: '3.8'
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install:
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- requirements: requirements.txt

‎README.md

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```matlab
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cd CPP_ROI
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% Th following adds the relevant folders to your path.
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% The following adds the relevant folders to your path.
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% This needs to be done once per session (your path will not be saved)
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initCppRoi
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- the SPM Anatomy toolbox (INSERT URL)
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- the SPM neuromorphometric atlas
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- neurosynth probability maps
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- A multi-modal parcellation of human cerebral cortex [@glasser_multi-modal_2016]
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- the probabilistic maps of visual topography in human cortex [@wang2014]
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- https://scholar.princeton.edu/napl/resources
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- the probabilistic functional atlas of human occipito-temporal visual

‎atlas/Glasser/LUT.csv

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label,description,ROI
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1,Primary_visual_cortex,V1
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2,Medial_superior_temporal_area,MST
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3,Sixth_Visual_Area,V6
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4,Second_Visual_Area,V2
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5,Third_Visual_Area,V3
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6,Forth_Visual_Area,V4
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7,Eighth_Visual_Area,V8
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8,Primary_Motor_Cortex,4
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9,Primary_Sensory_Cortex,3b
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10,Frontal_Eye_Field,FEF
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11,Premotor_Eye_Field,PEF
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12,Area_55b,55b
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13,Area_V3A,V3A
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14,RetroSplenial_Complex,RSC
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15,Parieto-Occipital_Sulcus_Area_2,POS2
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16,Seventh_Visual_Area,V7
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17,IntraParietal_Sulcus_Area_1,IPS1
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18,Fusiform_Face_Complex,FFC
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19,Area_V3B,V3B
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20,Lateral_Occipital_Area_1,LO1
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21,Lateral_Occipital_Area_2,LO2
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22,Posterior_InferoTemporal_Complex,PIT
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23,Middle_Temporal_Area,MT
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24,Primary_Auditory_Cortex,A1
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25,PeriSylvian_Language_Area,PSL
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26,Superior_Frontal_Language_Area,SFL
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27,PreCuneus_Visual_Area,PCV
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28,Superior_Temporal_Visual_Area,STV
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29,Medial_Area_7P,7Pm
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30,Area_7m,7m
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31,Parieto-Occipital_Sulcus_Area_1,POS1
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32,Area_23d,23d
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33,Area_Ventral_23_a,+bv23ab
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34,Area_Dorsal_23_a,+bd23ab
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35,Area_31p_Ventral,31pv
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36,Area_5m,5m
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37,Area_5m_ventral,5mv
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38,Area_23c,23c
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39,Area_5L,5L
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40,Dorsal_Area_24d,24dd
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41,Lateral_Area_7A,24dv
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42,Supplementary_and_Cingulate_Eye_Field,7AL
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43,Area_6m_Anterior,SCEF
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44,Medial_6m_anterior,6ma
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45,Medial_Area_7A,7Am
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46,Lateral_Area_7P,7PL
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47,Area_7PC,7PC
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48,Area_Lateral_IntraParietal_ventral,LIPv
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49,Ventral_IntraParietal_Complex,VIP
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50,Medial_IntraParietal_Area,MIP
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51,Area_1,1
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52,Area_2,2
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53,Area_3a,3a
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54,Dorsal_area_6,6d
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55,Area_6mp,6mp
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56,Ventral_Area_6,6v
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57,Area_Posterior_24,p24pr
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58,Area_33_prime,33pr
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59,Anterior_24_prime,a24pr
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60,Area_p32_prime,p32pr
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61,Area_a24,a24
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62,Area_dorsal_32,d32
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63,Area_8BM,8BM
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64,Area_p32,p32
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65,Area_10r,10r
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66,Area_47m,47m
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67,Area_8Av,8Av
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68,Area_8Ad,8Ad
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69,Area_9_Middle,9m
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70,Area_8B_Lateral,8BL
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71,Area_9_Posterior,9p
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72,Area_10d,10d
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73,Area_8C,8C
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74,Area_44,44
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75,Area_45,45
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76,Area_47L,47l
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77,Area_anterior_47R,a47r
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78,Rostral_Area_6,6r
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79,Area_IFJa,IFJa
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80,Area_IFJp,IFJp
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81,Area_IFSp,IFSp
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82,Area_IFSa,IFSa
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83,Area_posterior_9-46v,p9-46v
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84,Area_46,46
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85,Area_anterior_9-46v,a9-46v
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86,Area_9-46d,9-46d
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87,Area_9_anterior,9a
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88,Area_10v,10v
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89,Area_anterior_10p,a10p
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90,Polar_10p,10pp
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91,Area_11,11l
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92,Area_13,13l
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93,Orbital_Frontal_Complex,OFC
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94,Area_47s,47s
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95,Area_Lateral_IntraParietal_dorsal,LIPd
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96,Area_6_anterior,6a
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97,Inferior_6-8_Transitional_Area,i6-8
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98,Superior_6-8_Transitional_Area,s6-8
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99,Area_43,43
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100,Area_OP4/PV,OP4
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101,Area_OP1/SII,OP1
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102,Area_OP2-3/VS,OP2-3
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103,Area_52,52
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104,RetroInsular_Cortex,RI
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105,Area_PFcm,PFcm
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106,Posterior_Insular_Area_2,PoI2
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107,Area_TA2,TA2
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108,Frontal_OPercular_Area_4,FOP4
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109,Middle_Insular_Area,MI
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110,Pirform_Cortex,Pir
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111,Anterior_Ventral_Insular_Area,AVI
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112,Anterior_Agranular_Insula_Complex,AAIC
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113,Frontal_OPercular_Area_1,FOP1
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114,Frontal_OPercular_Area_3,FOP3
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115,Frontal_OPercular_Area_2,FOP2
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116,Area_PFt,PFt
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117,Anterior_IntraParietal_Area,AIP
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118,Entorhinal_Cortex,EC
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119,PreSubiculum,PreS
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120,Hippocampus,H
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121,ProStraite_Area,ProS
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122,Perirhinal_Ectorhinal_Cortex,PeEc
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123,Area_STGa,STGa
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124,ParaBelt_Complex,PBelt
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125,Auditory_5_Complex,A5
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126,ParaHippocampal_Area_1,PHA1
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127,ParaHippocampal_Area_3,PHA3
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128,Area_STSd_Anterior,STSda
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129,Area_STSd_Posterior,STSdp
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130,Area_STSv_Posterior,STSvp
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131,Area_TG_Dorsal,TGd
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132,Area_TE1_Anterior,TE1a
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133,Area_TE1_Posterior,TE1p
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134,Area_TE2_Anterior,TE2a
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135,Area_TF,TF
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136,Area_TE2_Posterior,TE2p
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137,Area_PHT,PHT
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138,Area_PH,PH
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139,Area_TemporoParietoOccipital_Junction_1,TPOJ1
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140,Area_TemporoParietoOccipital_Junction_2,TPOJ2
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141,Area_TemporoParietoOccipital_Junction_3,TPOJ3
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142,Dorsal_Transitional_Visual_Area,DVT
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143,Area_PGp,PGp
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144,Area_IntraParietal_2,IP2
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145,Area_IntraParietal_1,IP1
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146,Area_IntraParietal_0,IP0
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147,Area_PF_Opercular,PFop
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148,Area_PF_Complex,PF
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149,Area_PFm_Complex,PFm
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150,Area_PGi,PGi
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151,Area_PGs,PGs
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152,Area_V6A,V6A
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153,VentroMedial_Visual_Area_1,VMV1
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154,VentroMedial_Visual_Area_3,VMV3
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155,ParaHippocampal_Area_2,PHA2
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156,Area_V4t,V4t
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157,Area_FST,FST
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158,Area_V3CD,V3CD
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159,Area_Lateral_Occipital_3,LO3
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160,VentroMedial_Visual_Area_2,VMV2
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161,Area_31pd,31pd
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162,Area_31a,31a
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163,Ventral_Visual_Complex,VVC
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164,Area_25,25
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165,Area_s32,s32
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166,Posterior_OFC_Complex,pOFC
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167,Area_Posterior_Insular_1,PoI1
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168,Insular_Granular_Complex,Ig
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169,Area_Frontal_Opercular_5,FOP5
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170,Area_Posterior_10p,p10p
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171,Area_Posterior_47r,p47r
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172,Area_TG_ventral,TGv
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173,Medial_Belt_Complex,MBelt
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174,Lateral_Belt_Complex,LBelt
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175,Auditory_4_Complex,A4
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176,Area_STSv_Anterior,STSva
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177,Area_TE1_Middle,TE1m
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178,Para-Insular_Area,PI
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179,Area_Anterior_32_Prime,a32pr
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180,Area_Posterior_24,p24

‎atlas/Glasser/README.md

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Taken from:
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https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_MNI2009a_GM_volumetric_in_NIfTI_format/3501911
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A volumetric version in MNI/ICBM 152 2009b NLIN Asymmetric space
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Label description were taken from:
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https://github.com/neurodata/neuroparc/blob/master/atlases/label/Human/Anatomical-labels-csv/Glasser.csv
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Related citations:
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Glasser, M. F., Coalson, T. S., Robinson, E. C., Hacker, C. D., Harwell, J.,
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Yacoub, E., et al. (2016). A multi-modal parcellation of human cerebral cortex.
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Nature. http://doi.org/10.1038/nature18933
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Based on the Freesurfer version of the HCP-MMP1.0 parcellation
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(https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446), I
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created a volumetric version of the HCP-MMP1.0 parcellation that was published
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by Glasser et al. (Nature, 2016).
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Please note that this volumetric version should be used and applied with great
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care – and under certain circumstances only. According to the authors of the
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original work, this fine parcellation could not have been achieved on a
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volumetric basis but was only realizable using a multimodal surface-based
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analysis (and co-registration). Thus, this volumetric version of their work is
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not ideally suited to be used for standard brain-mapping approaches that use
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(volumetric) nonlinear deformations. It is rather thought to be an accompanying
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volumetric version to the surface-based version. Also, it could be used for
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comparative purposes within MNI space (e.g. to compare it to other cortical
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parcellations available in this space such as the AAL, Hammersmith, AICHA,
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Mindboggle 101 atlases).
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The conversion to volumetric space (projection to the ICBM 152 2009a NLIN
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version within MNI space) is based on the fsaverage version of the HCP-MMP1.0
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available here
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(https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446).

‎atlas/Glasser/space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii.gz

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