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config.py
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config.py
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INPUT_FILE = 'input/DK_template.csv' # input template should match ATLAS below
OUTPUT_FOLDER = 'output/DK_output'
# either 'DK', 'Destrieux', 'Tourville', 'Mice', 'Dorr', 'Dsurque' or 'Custom'
ATLAS = 'DK'
# either 'pial' (with gyri/sulci), 'inflated' (smooth) or 'white' (white-matter surface)
BRAIN_TYPE = 'pial'
# either cortical-outer, cortical-inner, subcortical
# add -right-hemisphere or -left-hemisphere to end of image type to specify view
# image types "top" and "bottom" are available to show asymmetry
IMG_TYPE = 'top'
# what colours to use for showing brain pathology
# e.g. if the range of pathology is [0,3],
# then you need four colors (the first one is for pathology 0, i.e. no pathology)
# a pathology at 1.3 will interpolate between the second and third color
# NOTE: you can add more than 4 colours (as many as you want), in which case you should increase the range of the input biomarkers.
COLORS_RGB = [(1,1,1), (1,1,0), (1,0.4,0), (1,0,0)] # white -> yellow -> orange -> red
# COLORS_RGB = [(1,1,1), (1,0,0), (1,0,0), (1,0,0)] # white -> red -> red -> red
# output image resolution for X,Y in pixels
RESOLUTION = (1200, 900)
# default is white
BACKGROUND_COLOR = (1,1,1)
# to change camera viewing angle and other advanced settings, look into blendHelper.py:setCamera()
# for luminosity settings, look into blendHelper.py:setLamp()
if ATLAS == 'Mice' or ATLAS == 'Dorr' or ATLAS == 'Dsurque':
# we do not have white/inflated for mice yet
BRAIN_TYPE = 'pial'
### Advanced settings, only change if you want to use custom atlas or if you'd like to not color at all some regions #####
# map the names of each 3D cortical structure to be coloured to the name of the structure you have in your atlas.
# only change the right-hand side values, as the left-hand side are used by blender.
# Common customisations:
# 1. to completely remove a region from being displayed, remove both the (key,value) pair.
# 2. to deactivate a region (always color it in default dark gray color), map its value to -1
# NOTE: Always make sure the RHS regions (dict values) below are present in your input .csv file.
### DK atlas ###
# Left-Hand-Side = Blender Regions Right-Hand-Side = Regions in custom input atlas (.csv INPUT_FILE)
# disable any regions by setting its RHS to -1
cortAreasIndexMapDK = {
'Right-bankssts':'Right-bankssts',
'Right-caudalanteriorcingulate':'Right-caudalanteriorcingulate',
'Right-caudalmiddlefrontal':'Right-caudalmiddlefrontal',
'Right-cuneus':'Right-cuneus',
'Right-entorhinal':'Right-entorhinal',
'Right-frontalpole': 'Right-frontalpole',
'Right-fusiform':'Right-fusiform',
'Right-inferiorparietal':'Right-inferiorparietal',
'Right-inferiortemporal':'Right-inferiortemporal',
'Right-insula':'Right-insula',
'Right-isthmuscingulate':'Right-isthmuscingulate',
'Right-lateraloccipital':'Right-lateraloccipital',
'Right-lateralorbitofrontal':'Right-lateralorbitofrontal',
'Right-lingual':'Right-lingual',
'Right-medialorbitofrontal':'Right-medialorbitofrontal',
'Right-middletemporal':'Right-middletemporal',
'Right-paracentral':'Right-paracentral',
'Right-parahippocampal':'Right-parahippocampal',
'Right-parsopercularis':'Right-parsopercularis',
'Right-parsorbitalis':'Right-parsorbitalis',
'Right-parstriangularis':'Right-parstriangularis',
'Right-pericalcarine':'Right-pericalcarine',
'Right-postcentral':'Right-postcentral',
'Right-posteriorcingulate':'Right-posteriorcingulate',
'Right-precentral':'Right-precentral',
'Right-precuneus':'Right-precuneus',
'Right-rostralanteriorcingulate':'Right-rostralanteriorcingulate',
'Right-rostralmiddlefrontal':'Right-rostralmiddlefrontal',
'Right-superiorfrontal':'Right-superiorfrontal',
'Right-superiorparietal':'Right-superiorparietal',
'Right-superiortemporal':'Right-superiortemporal',
'Right-supramarginal':'Right-supramarginal',
'Right-temporalpole':'Right-temporalpole',
'Right-transversetemporal':'Right-transversetemporal',
'Right-unknown':-1, # this is actually the middle region inside the cortical surface. color it as gray
'Left-bankssts':'Left-bankssts',
'Left-caudalanteriorcingulate':'Left-caudalanteriorcingulate',
'Left-caudalmiddlefrontal':'Left-caudalmiddlefrontal',
'Left-cuneus':'Left-cuneus',
'Left-entorhinal':'Left-entorhinal',
'Left-frontalpole': 'Left-frontalpole',
'Left-fusiform':'Left-fusiform',
'Left-inferiorparietal':'Left-inferiorparietal',
'Left-inferiortemporal':'Left-inferiortemporal',
'Left-insula':'Left-insula',
'Left-isthmuscingulate':'Left-isthmuscingulate',
'Left-lateraloccipital':'Left-lateraloccipital',
'Left-lateralorbitofrontal':'Left-lateralorbitofrontal',
'Left-lingual':'Left-lingual',
'Left-medialorbitofrontal':'Left-medialorbitofrontal',
'Left-middletemporal':'Left-middletemporal',
'Left-paracentral':'Left-paracentral',
'Left-parahippocampal':'Left-parahippocampal',
'Left-parsopercularis':'Left-parsopercularis',
'Left-parsorbitalis':'Left-parsorbitalis',
'Left-parstriangularis':'Left-parstriangularis',
'Left-pericalcarine':'Left-pericalcarine',
'Left-postcentral':'Left-postcentral',
'Left-posteriorcingulate':'Left-posteriorcingulate',
'Left-precentral':'Left-precentral',
'Left-precuneus':'Left-precuneus',
'Left-rostralanteriorcingulate':'Left-rostralanteriorcingulate',
'Left-rostralmiddlefrontal':'Left-rostralmiddlefrontal',
'Left-superiorfrontal':'Left-superiorfrontal',
'Left-superiorparietal':'Left-superiorparietal',
'Left-superiortemporal':'Left-superiortemporal',
'Left-supramarginal':'Left-supramarginal',
'Left-temporalpole':'Left-temporalpole',
'Left-transversetemporal':'Left-transversetemporal',
'Left-unknown':-1 # this is actually the middle region inside the cortical surface. color it as gray
}
### Destrieux atlas ###
# Left-Hand-Side = Blender Regions Right-Hand-Side = Regions in custom input atlas (.csv INPUT_FILE)
cortAreasIndexMapDestrieux = {
'Right-G_and_S_frontomargin': 'Right-G_and_S_frontomargin',
'Right-G_and_S_occipital_inf': 'Right-G_and_S_occipital_inf',
'Right-G_and_S_paracentral': 'Right-G_and_S_paracentral',
'Right-G_and_S_subcentral': 'Right-G_and_S_subcentral',
'Right-G_and_S_transv_frontopol': 'Right-G_and_S_transv_frontopol' ,
'Right-G_and_S_cingul-Ant': 'Right-G_and_S_cingul-Ant',
'Right-G_and_S_cingul-Mid-Ant': 'Right-G_and_S_cingul-Mid-Ant',
'Right-G_and_S_cingul-Mid-Post': 'Right-G_and_S_cingul-Mid-Post',
'Right-G_cingul-Post-dorsal': 'Right-G_cingul-Post-dorsal',
'Right-G_cingul-Post-ventral': 'Right-G_cingul-Post-ventral',
'Right-G_cuneus': 'Right-G_cuneus',
'Right-G_front_inf-Opercular': 'Right-G_front_inf-Opercular',
'Right-G_front_inf-Orbital': 'Right-G_front_inf-Orbital',
'Right-G_front_inf-Triangul': 'Right-G_front_inf-Triangul' ,
'Right-G_front_middle': 'Right-G_front_middle',
'Right-G_front_sup': 'Right-G_front_sup',
'Right-G_Ins_lg_and_S_cent_ins': 'Right-G_Ins_lg_and_S_cent_ins',
'Right-G_insular_short': 'Right-G_insular_short',
'Right-G_occipital_middle': 'Right-G_occipital_middle',
'Right-G_occipital_sup': 'Right-G_occipital_sup',
'Right-G_oc-temp_lat-fusifor': 'Right-G_oc-temp_lat-fusifor',
'Right-G_oc-temp_med-Lingual': 'Right-G_oc-temp_med-Lingual' ,
'Right-G_oc-temp_med-Parahip': 'Right-G_oc-temp_med-Parahip' ,
'Right-G_orbital': 'Right-G_orbital',
'Right-G_pariet_inf-Angular': 'Right-G_pariet_inf-Angular',
'Right-G_pariet_inf-Supramar': 'Right-G_pariet_inf-Supramar',
'Right-G_parietal_sup': 'Right-G_parietal_sup',
'Right-G_postcentral': 'Right-G_postcentral',
'Right-G_precentral': 'Right-G_precentral',
'Right-G_precuneus': 'Right-G_precuneus',
'Right-G_rectus': 'Right-G_rectus',
'Right-G_subcallosal': 'Right-G_subcallosal',
'Right-G_temp_sup-G_T_transv': 'Right-G_temp_sup-G_T_transv',
'Right-G_temp_sup-Lateral': 'Right-G_temp_sup-Lateral',
'Right-G_temp_sup-Plan_polar': 'Right-G_temp_sup-Plan_polar' ,
'Right-G_temp_sup-Plan_tempo': 'Right-G_temp_sup-Plan_tempo' ,
'Right-G_temporal_inf': 'Right-G_temporal_inf',
'Right-G_temporal_middle': 'Right-G_temporal_middle',
'Right-Lat_Fis-ant-Horizont': 'Right-Lat_Fis-ant-Horizont',
'Right-Lat_Fis-ant-Vertical': 'Right-Lat_Fis-ant-Vertical',
'Right-Lat_Fis-post': 'Right-Lat_Fis-post',
'Right-Pole_occipital': 'Right-Pole_occipital',
'Right-Pole_temporal': 'Right-Pole_temporal',
'Right-S_calcarine': 'Right-S_calcarine',
'Right-S_central': 'Right-S_central',
'Right-S_cingul-Marginalis': 'Right-S_cingul-Marginalis',
'Right-S_circular_insula_ant': 'Right-S_circular_insula_ant',
'Right-S_circular_insula_inf': 'Right-S_circular_insula_inf',
'Right-S_circular_insula_sup': 'Right-S_circular_insula_sup',
'Right-S_collat_transv_ant': 'Right-S_collat_transv_ant',
'Right-S_collat_transv_post': 'Right-S_collat_transv_post',
'Right-S_front_inf': 'Right-S_front_inf',
'Right-S_front_middle': 'Right-S_front_middle',
'Right-S_front_sup': 'Right-S_front_sup',
'Right-S_interm_prim-Jensen': 'Right-S_interm_prim-Jensen',
'Right-S_intrapariet_and_P_trans': 'Right-S_intrapariet_and_P_trans',
'Right-S_oc_middle_and_Lunatus': 'Right-S_oc_middle_and_Lunatus',
'Right-S_oc_sup_and_transversal': 'Right-S_oc_sup_and_transversal',
'Right-S_occipital_ant': 'Right-S_occipital_ant',
'Right-S_oc-temp_lat': 'Right-S_oc-temp_lat',
'Right-S_oc-temp_med_and_Lingual': 'Right-S_oc-temp_med_and_Lingual',
'Right-S_orbital_lateral': 'Right-S_orbital_lateral',
'Right-S_orbital_med-olfact': 'Right-S_orbital_med-olfact',
'Right-S_orbital-H_Shaped': 'Right-S_orbital-H_Shaped',
'Right-S_parieto_occipital': 'Right-S_parieto_occipital',
'Right-S_pericallosal': 'Right-S_pericallosal',
'Right-S_postcentral': 'Right-S_postcentral',
'Right-S_precentral-inf-part': 'Right-S_precentral-inf-part',
'Right-S_precentral-sup-part': 'Right-S_precentral-sup-part',
'Right-S_suborbital': 'Right-S_suborbital',
'Right-S_subparietal': 'Right-S_subparietal',
'Right-S_temporal_inf': 'Right-S_temporal_inf',
'Right-S_temporal_sup': 'Right-S_temporal_sup',
'Right-S_temporal_transverse': 'Right-S_temporal_transverse',
'Right-Unknown':-1, # this is actually the middle region inside the cortical surface. color it as gray
'Left-G_and_S_frontomargin': 'Left-G_and_S_frontomargin',
'Left-G_and_S_occipital_inf': 'Left-G_and_S_occipital_inf',
'Left-G_and_S_paracentral': 'Left-G_and_S_paracentral',
'Left-G_and_S_subcentral': 'Left-G_and_S_subcentral',
'Left-G_and_S_transv_frontopol': 'Left-G_and_S_transv_frontopol' ,
'Left-G_and_S_cingul-Ant': 'Left-G_and_S_cingul-Ant',
'Left-G_and_S_cingul-Mid-Ant': 'Left-G_and_S_cingul-Mid-Ant',
'Left-G_and_S_cingul-Mid-Post': 'Left-G_and_S_cingul-Mid-Post',
'Left-G_cingul-Post-dorsal': 'Left-G_cingul-Post-dorsal',
'Left-G_cingul-Post-ventral': 'Left-G_cingul-Post-ventral',
'Left-G_cuneus': 'Left-G_cuneus',
'Left-G_front_inf-Opercular': 'Left-G_front_inf-Opercular',
'Left-G_front_inf-Orbital': 'Left-G_front_inf-Orbital',
'Left-G_front_inf-Triangul': 'Left-G_front_inf-Triangul' ,
'Left-G_front_middle': 'Left-G_front_middle',
'Left-G_front_sup': 'Left-G_front_sup',
'Left-G_Ins_lg_and_S_cent_ins': 'Left-G_Ins_lg_and_S_cent_ins',
'Left-G_insular_short': 'Left-G_insular_short',
'Left-G_occipital_middle': 'Left-G_occipital_middle',
'Left-G_occipital_sup': 'Left-G_occipital_sup',
'Left-G_oc-temp_lat-fusifor': 'Left-G_oc-temp_lat-fusifor',
'Left-G_oc-temp_med-Lingual': 'Left-G_oc-temp_med-Lingual' ,
'Left-G_oc-temp_med-Parahip': 'Left-G_oc-temp_med-Parahip' ,
'Left-G_orbital': 'Left-G_orbital',
'Left-G_pariet_inf-Angular': 'Left-G_pariet_inf-Angular',
'Left-G_pariet_inf-Supramar': 'Left-G_pariet_inf-Supramar',
'Left-G_parietal_sup': 'Left-G_parietal_sup',
'Left-G_postcentral': 'Left-G_postcentral',
'Left-G_precentral': 'Left-G_precentral',
'Left-G_precuneus': 'Left-G_precuneus',
'Left-G_rectus': 'Left-G_rectus',
'Left-G_subcallosal': 'Left-G_subcallosal',
'Left-G_temp_sup-G_T_transv': 'Left-G_temp_sup-G_T_transv',
'Left-G_temp_sup-Lateral': 'Left-G_temp_sup-Lateral',
'Left-G_temp_sup-Plan_polar': 'Left-G_temp_sup-Plan_polar' ,
'Left-G_temp_sup-Plan_tempo': 'Left-G_temp_sup-Plan_tempo' ,
'Left-G_temporal_inf': 'Left-G_temporal_inf',
'Left-G_temporal_middle': 'Left-G_temporal_middle',
'Left-Lat_Fis-ant-Horizont': 'Left-Lat_Fis-ant-Horizont',
'Left-Lat_Fis-ant-Vertical': 'Left-Lat_Fis-ant-Vertical',
'Left-Lat_Fis-post': 'Left-Lat_Fis-post',
'Left-Pole_occipital': 'Left-Pole_occipital',
'Left-Pole_temporal': 'Left-Pole_temporal',
'Left-S_calcarine': 'Left-S_calcarine',
'Left-S_central': 'Left-S_central',
'Left-S_cingul-Marginalis': 'Left-S_cingul-Marginalis',
'Left-S_circular_insula_ant': 'Left-S_circular_insula_ant',
'Left-S_circular_insula_inf': 'Left-S_circular_insula_inf',
'Left-S_circular_insula_sup': 'Left-S_circular_insula_sup',
'Left-S_collat_transv_ant': 'Left-S_collat_transv_ant',
'Left-S_collat_transv_post': 'Left-S_collat_transv_post',
'Left-S_front_inf': 'Left-S_front_inf',
'Left-S_front_middle': 'Left-S_front_middle',
'Left-S_front_sup': 'Left-S_front_sup',
'Left-S_interm_prim-Jensen': 'Left-S_interm_prim-Jensen',
'Left-S_intrapariet_and_P_trans': 'Left-S_intrapariet_and_P_trans',
'Left-S_oc_middle_and_Lunatus': 'Left-S_oc_middle_and_Lunatus',
'Left-S_oc_sup_and_transversal': 'Left-S_oc_sup_and_transversal',
'Left-S_occipital_ant': 'Left-S_occipital_ant',
'Left-S_oc-temp_lat': 'Left-S_oc-temp_lat',
'Left-S_oc-temp_med_and_Lingual': 'Left-S_oc-temp_med_and_Lingual',
'Left-S_orbital_lateral': 'Left-S_orbital_lateral',
'Left-S_orbital_med-olfact': 'Left-S_orbital_med-olfact',
'Left-S_orbital-H_Shaped': 'Left-S_orbital-H_Shaped',
'Left-S_parieto_occipital': 'Left-S_parieto_occipital',
'Left-S_pericallosal': 'Left-S_pericallosal',
'Left-S_postcentral': 'Left-S_postcentral',
'Left-S_precentral-inf-part': 'Left-S_precentral-inf-part',
'Left-S_precentral-sup-part': 'Left-S_precentral-sup-part',
'Left-S_suborbital': 'Left-S_suborbital',
'Left-S_subparietal': 'Left-S_subparietal',
'Left-S_temporal_inf': 'Left-S_temporal_inf',
'Left-S_temporal_sup': 'Left-S_temporal_sup',
'Left-S_temporal_transverse': 'Left-S_temporal_transverse',
'Left-Unknown':-1, # this is actually the middle region inside the cortical surface. color it as gray
}
### Mouse brain atlas ###
# Left-Hand-Side = Blender Regions Right-Hand-Side = Regions in custom input atlas (.csv INPUT_FILE)
cortAreasIndexMapMice = {
'Right-Anterior-cingulate': 'Right-Anterior-cingulate',
'Right-Auditory': 'Right-Auditory',
'Right-Cortical-subplate': 'Right-Cortical-subplate',
'Right-Gustatory': 'Right-Gustatory',
'Right-Infralimbic': 'Right-Infralimbic',
'Right-Medulla': 'Right-Medulla',
'Right-Olfactory': 'Right-Olfactory',
'Right-Pons': 'Right-Pons',
'Right-Prelimbic': 'Right-Prelimbic',
'Right-Retrosplenial': 'Right-Retrosplenial',
'Right-Somatomotor': 'Right-Somatomotor',
'Right-Somatosensory': 'Right-Somatosensory',
'Right-Striatum': 'Right-Striatum',
'Right-Visceral': 'Right-Visceral',
'Right-Visual': 'Right-Visual',
'Right-Agranular-insular-area': 'Right-Agranular-insular-area',
'Right-Posterior-parietal-association-areas': 'Right-Posterior-parietal-association-areas',
'Right-Temporal-association-areas': 'Right-Temporal-association-areas',
'Right-Perirhinal': 'Right-Perirhinal',
'Right-Ectorhinal': 'Right-Ectorhinal',
'Left-Anterior-cingulate': 'Left-Anterior-cingulate',
'Left-Auditory': 'Left-Auditory',
'Left-Cortical-subplate': 'Left-Cortical-subplate',
'Left-Gustatory': 'Left-Gustatory',
'Left-Infralimbic': 'Left-Infralimbic',
'Left-Medulla': 'Left-Medulla',
'Left-Olfactory': 'Left-Olfactory',
'Left-Pons': 'Left-Pons',
'Left-Prelimbic': 'Left-Prelimbic',
'Left-Retrosplenial': 'Left-Retrosplenial',
'Left-Somatomotor': 'Left-Somatomotor',
'Left-Somatosensory': 'Left-Somatosensory',
'Left-Striatum': 'Left-Striatum',
'Left-Visceral': 'Left-Visceral',
'Left-Visual': 'Left-Visual',
'Left-Agranular-insular-area': 'Left-Agranular-insular-area',
'Left-Posterior-parietal-association-areas': 'Left-Posterior-parietal-association-areas',
'Left-Temporal-association-areas': 'Left-Temporal-association-areas',
'Left-Perirhinal': 'Left-Perirhinal',
'Left-Ectorhinal': 'Left-Ectorhinal',
}
# subcortical areas for mouse atlas
subcortMouseAreasIndexMap = {
'Left-Cerebellum':'Left-Cerebellum', # -1 means do not colour this region
'Left-Hypothalamus':'Left-Hypothalamus',
'Left-Frontal-pole': 'Left-Frontal-pole', # Acronym for Frontal pole, cerebral cortex,
'Left-Hippocampus': 'Left-Hippocampus',
'Left-Midbrain':'Left-Midbrain',
'Left-Pallidum': 'Left-Pallidum',
'Left-Thalamus':'Left-Thalamus',
'Right-Cerebellum':'Right-Cerebellum', # -1 means do not colour this region
'Right-Hypothalamus':'Right-Hypothalamus',
'Right-Frontal-pole': 'Right-Frontal-pole', # Acronym for Frontal pole, cerebral cortex,
'Right-Hippocampus': 'Right-Hippocampus',
'Right-Midbrain':'Right-Midbrain',
'Right-Pallidum': 'Right-Pallidum',
'Right-Thalamus':'Right-Thalamus'
}
# subcortical regions for the dorr atlas
subcortDorrAreasIndexMap = {
'bilateral_cerebral_aqueduct': 'bilateral_cerebral_aqueduct',
'bilateral_fourth_ventricle': 'bilateral_fourth_ventricle',
'bilateral_interpedunclar_nucleus': 'bilateral_interpedunclar_nucleus',
'bilateral_medulla': 'bilateral_medulla',
'bilateral_midbrain': 'bilateral_midbrain',
'bilateral_periaqueductal_grey': 'bilateral_periaqueductal_grey',
'bilateral_pons': 'bilateral_pons',
'bilateral_posterior_commissure': 'bilateral_posterior_commissure',
'bilateral_third_ventricle': 'bilateral_third_ventricle',
'bilateral_ventral_tegmental_decussation': 'bilateral_ventral_tegmental_decussation',
}
# subcortical regions for the dsurque atlas
subcortDsurqueAreasIndexMap = {
'bilateral_cerebral_aqueduct': 'bilateral_cerebral_aqueduct',
'bilateral_fourth_ventricle': 'bilateral_fourth_ventricle',
'bilateral_interpedunclar_nucleus': 'bilateral_interpedunclar_nucleus',
'bilateral_lobule_10_nodulus': 'bilateral_lobule_10_nodulus',
'bilateral_lobule_10_white_matter': 'bilateral_lobule_10_white_matter',
'bilateral_lobule_1_2_white_matter': 'bilateral_lobule_1_2_white_matter',
'bilateral_lobule_3_central_lobule_dorsal': 'bilateral_lobule_3_central_lobule_dorsal',
'bilateral_lobule_3_white_matter': 'bilateral_lobule_3_white_matter',
'bilateral_lobule_6_declive': 'bilateral_lobule_6_declive',
'bilateral_lobule_7_tuber_or_folium': 'bilateral_lobule_7_tuber_or_folium',
'bilateral_lobule_8_pyramis': 'bilateral_lobule_8_pyramis',
'bilateral_lobule_8_white_matter': 'bilateral_lobule_8_white_matter',
'bilateral_lobule_9_uvula': 'bilateral_lobule_9_uvula',
'bilateral_lobule_9_white_matter': 'bilateral_lobule_9_white_matter',
'bilateral_lobules_1_2_lingula_and_central_lobule_ventral': 'bilateral_lobules_1_2_lingula_and_central_lobule_ventral',
'bilateral_lobules_4_5_culmen_ventral_and_dorsal': 'bilateral_lobules_4_5_culmen_ventral_and_dorsal',
'bilateral_lobules_4_5_white_matter': 'bilateral_lobules_4_5_white_matter',
'bilateral_lobules_6_7_white_matter': 'bilateral_lobules_6_7_white_matter',
'bilateral_medulla': 'bilateral_medulla',
'bilateral_midbrain': 'bilateral_midbrain',
'bilateral_periaqueductal_grey': 'bilateral_periaqueductal_grey',
'bilateral_pons': 'bilateral_pons',
'bilateral_posterior_commissure': 'bilateral_posterior_commissure',
'bilateral_third_ventricle': 'bilateral_third_ventricle',
'bilateral_trunk_of_arbor_vita': 'bilateral_trunk_of_arbor_vita',
'bilateral_trunk_of_lobules_1_3_white_matter': 'bilateral_trunk_of_lobules_1_3_white_matter',
'bilateral_trunk_of_lobules_6_8_white_matter': 'bilateral_trunk_of_lobules_6_8_white_matter',
'bilateral_ventral_tegmental_decussation': 'bilateral_ventral_tegmental_decussation',
}
cortAreasIndexMapDsurque = {
'Left-accessory_olfactory_bulb_glomerular_external_plexiform_and_mitral_cell_layer': 'Left-accessory_olfactory_bulb_glomerular_external_plexiform_and_mitral_cell_layer',
'Left-accessory_olfdactory_bulb_granule_cell_layer': 'Left-accessory_olfactory_bulb_granule_cell_layer',
'Left-amygdala': 'Left-amygdala',
'Left-amygdalopiriform_transition_area': 'Left-amygdalopiriform_transition_area',
'Left-anterior_commissure_pars_anterior': 'Left-anterior_commissure_pars_anterior',
'Left-anterior_commissure_pars_posterior': 'Left-anterior_commissure_pars_posterior',
'Left-anterior_lobule_lobules_4_5': 'Left-anterior_lobule_lobules_4_5',
'Left-anterior_lobule_white_matter': 'Left-anterior_lobule_white_matter',
'Left-anterior_olfactory_nucleus': 'Left-anterior_olfactory_nucleus',
'Left-basal_forebrain': 'Left-basal_forebrain',
'Left-bed_nucleus_of_stria_terminalis': 'Left-bed_nucleus_of_stria_terminalis',
'Left-ca10r': 'Left-ca10r',
'Left-ca1py': 'Left-ca1py',
'Left-ca1rad': 'Left-ca1rad',
'Left-ca20r': 'Left-ca20r',
'Left-ca2py': 'Left-ca2py',
'Left-ca2rad': 'Left-ca2rad',
'Left-ca30r': 'Left-ca30r',
'Left-ca3py_inner': 'Left-ca3py_inner',
'Left-ca3py_outer': 'Left-ca3py_outer',
'Left-ca3rad': 'Left-ca3rad',
'Left-caudomedial_entorhinal_cortex': 'Left-caudomedial_entorhinal_cortex',
'Left-cerebellar_peduncle_inferior': 'Left-cerebellar_peduncle_inferior',
'Left-cerebellar_peduncle_middle': 'Left-cerebellar_peduncle_middle',
'Left-cerebellar_peduncle_superior': 'Left-cerebellar_peduncle_superior',
'Left-cerebral_peduncle': 'Left-cerebral_peduncle',
'Left-cingulate_cortex_area_24a': 'Left-cingulate_cortex_area_24a',
'Left-cingulate_cortex_area_24a_2': 'Left-cingulate_cortex_area_24a_2',
'Left-cingulate_cortex_area_24b': 'Left-cingulate_cortex_area_24b',
'Left-cingulate_cortex_area_24b_2': 'Left-cingulate_cortex_area_24b_2',
'Left-cingulate_cortex_area_25': 'Left-cingulate_cortex_area_25',
'Left-cingulate_cortex_area_29a': 'Left-cingulate_cortex_area_29a',
'Left-cingulate_cortex_area_29b': 'Left-cingulate_cortex_area_29b',
'Left-cingulate_cortex_area_29c': 'Left-cingulate_cortex_area_29c',
'Left-cingulate_cortex_area_30': 'Left-cingulate_cortex_area_30',
'Left-cingulate_cortex_area_32': 'Left-cingulate_cortex_area_32',
'Left-cingulum': 'Left-cingulum',
'Left-claustrum': 'Left-claustrum',
'Left-claustrum_dorsal_part': 'Left-claustrum_dorsal_part',
'Left-claustrum_ventral_part': 'Left-claustrum_ventral_part',
'Left-colliculus_inferior': 'Left-colliculus_inferior',
'Left-colliculus_superior': 'Left-colliculus_superior',
'Left-copula_pyramis_lobule_8': 'Left-copula_pyramis_lobule_8',
'Left-copula_white_matter': 'Left-copula_white_matter',
'Left-corpus_callosum': 'Left-corpus_callosum',
'Left-cortex_amygdala_transition_zones': 'Left-cortex_amygdala_transition_zones',
'Left-corticospinal_tract_pyramids': 'Left-corticospinal_tract_pyramids',
'Left-crus_1_ansiform_lobule_lobule_6': 'Left-crus_1_ansiform_lobule_lobule_6',
'Left-crus_1_white_matter': 'Left-crus_1_white_matter',
'Left-crus_2_ansiform_lobule_lobule_7': 'Left-crus_2_ansiform_lobule_lobule_7',
'Left-crus_2_white_matter': 'Left-crus_2_white_matter',
'Left-cuneate_nucleus': 'Left-cuneate_nucleus',
'Left-dentate_nucleus': 'Left-dentate_nucleus',
'Left-dorsal_intermediate_entorhinal_cortex': 'Left-dorsal_intermediate_entorhinal_cortex',
'Left-dorsal_nucleus_of_the_endopiriform': 'Left-dorsal_nucleus_of_the_endopiriform',
'Left-dorsal_tenia_tecta': 'Left-dorsal_tenia_tecta',
'Left-dorsolateral_entorhinal_cortex': 'Left-dorsolateral_entorhinal_cortex',
'Left-dorsolateral_orbital_cortex': 'Left-dorsolateral_orbital_cortex',
'Left-ectorhinal_cortex': 'Left-ectorhinal_cortex',
'Left-facial_nerve_cranial_nerve_7': 'Left-facial_nerve_cranial_nerve_7',
'Left-fasciculus_retroflexus': 'Left-fasciculus_retroflexus',
'Left-fastigial_nucleus': 'Left-fastigial_nucleus',
'Left-fimbria': 'Left-fimbria',
'Left-flocculus_fl': 'Left-flocculus_fl',
'Left-flocculus_white_matter': 'Left-flocculus_white_matter',
'Left-fornix': 'Left-fornix',
'Left-frontal_association_cortex': 'Left-frontal_association_cortex',
'Left-frontal_cortex_area_3': 'Left-frontal_cortex_area_3',
'Left-fundus_of_striatum': 'Left-fundus_of_striatum',
'Left-globus_pallidus': 'Left-globus_pallidus',
'Left-gr_dg': 'Left-gr_dg',
'Left-habenular_commissure': 'Left-habenular_commissure',
'Left-hypothalamus': 'Left-hypothalamus',
'Left-inferior_olivary_complex': 'Left-inferior_olivary_complex',
'Left-insular_region_not_subdivided': 'Left-insular_region_not_subdivided',
'Left-intermediate_nucleus_of_the_endopiriform_claustrum': 'Left-intermediate_nucleus_of_the_endopiriform_claustrum',
'Left-internal_capsule': 'Left-internal_capsule',
'Left-l_mol': 'Left-l_mol',
'Left-lateral_olfactory_tract': 'Left-lateral_olfactory_tract',
'Left-lateral_orbital_cortex': 'Left-lateral_orbital_cortex',
'Left-lateral_parietal_association_cortex': 'Left-lateral_parietal_association_cortex',
'Left-lateral_septum': 'Left-lateral_septum',
'Left-lateral_ventricle': 'Left-lateral_ventricle',
'Left-mammillary_bodies': 'Left-mammillary_bodies',
'Left-mammilothalamic_tract': 'Left-mammilothalamic_tract',
'Left-medial_amygdala': 'Left-medial_amygdala',
'Left-medial_entorhinal_cortex': 'Left-medial_entorhinal_cortex',
'Left-medial_lemniscus_medial_longitudinal_fasciculus': 'Left-medial_lemniscus_medial_longitudinal_fasciculus',
'Left-medial_orbital_cortex': 'Left-medial_orbital_cortex',
'Left-medial_parietal_association_cortex': 'Left-medial_parietal_association_cortex',
'Left-medial_preoptic_nucleus': 'Left-medial_preoptic_nucleus',
'Left-medial_septum': 'Left-medial_septum',
'Left-mo_dg_Right': 'Left-mo_dg_Right',
'Left-nucleus_accumbens': 'Left-nucleus_accumbens',
'Left-nucleus_interpositus': 'Left-nucleus_interpositus',
'Left-olfactory_bulb_external_plexiform_layer': 'Left-olfactory_bulb_external_plexiform_layer',
'Left-olfactory_bulb_glomerular_layer': 'Left-olfactory_bulb_glomerular_layer',
'Left-olfactory_bulb_granule_cell_layer': 'Left-olfactory_bulb_granule_cell_layer',
'Left-olfactory_bulb_internal_plexiform_layer': 'Left-olfactory_bulb_internal_plexiform_layer',
'Left-olfactory_bulb_mitral_cell_layer': 'Left-olfactory_bulb_mitral_cell_layer',
'Left-olfactory_peduncle': 'Left-olfactory_peduncle',
'Left-olfactory_tubercle': 'Left-olfactory_tubercle',
'Left-optic_tract': 'Left-optic_tract',
'Left-paraflocculus_pfl': 'Left-paraflocculus_pfl',
'Left-paraflocculus_white_matter': 'Left-paraflocculus_white_matter',
'Left-paramedian_lobule': 'Left-paramedian_lobule',
'Left-paramedian_lobule_lobule_7': 'Left-paramedian_lobule_lobule_7',
'Left-parietal_cortex_posterior_area_rostral_part': 'Left-parietal_cortex_posterior_area_rostral_part',
'Left-perirhinal_cortex': 'Left-perirhinal_cortex',
'Left-piriform_cortex': 'Left-piriform_cortex',
'Left-po_dg': 'Left-po_dg',
'Left-pontine_nucleus': 'Left-pontine_nucleus',
'Left-posterolateral_cortical_amygdaloid_area': 'Left-posterolateral_cortical_amygdaloid_area',
'Left-posteromedial_cortical_amygdaloid_area': 'Left-posteromedial_cortical_amygdaloid_area',
'Left-pre_para_subiculum': 'Left-pre_para_subiculum',
'Left-primary_auditory_cortex': 'Left-primary_auditory_cortex',
'Left-primary_motor_cortex': 'Left-primary_motor_cortex',
'Left-primary_somatosensory_cortex': 'Left-primary_somatosensory_cortex',
'Left-primary_somatosensory_cortex_barrel_field': 'Left-primary_somatosensory_cortex_barrel_field',
'Left-primary_somatosensory_cortex_dysgranular_zone': 'Left-primary_somatosensory_cortex_dysgranular_zone',
'Left-primary_somatosensory_cortex_forelimb_region': 'Left-primary_somatosensory_cortex_forelimb_region',
'Left-primary_somatosensory_cortex_hindlimb_region': 'Left-primary_somatosensory_cortex_hindlimb_region',
'Left-primary_somatosensory_cortex_jaw_region': 'Left-primary_somatosensory_cortex_jaw_region',
'Left-primary_somatosensory_cortex_shoulder_region': 'Left-primary_somatosensory_cortex_shoulder_region',
'Left-primary_somatosensory_cortex_trunk_region': 'Left-primary_somatosensory_cortex_trunk_region',
'Left-primary_somatosensory_cortex_upper_lip_region': 'Left-primary_somatosensory_cortex_upper_lip_region',
'Left-primary_visual_cortex': 'Left-primary_visual_cortex',
'Left-primary_visual_cortex_binocular_area': 'Left-primary_visual_cortex_binocular_area',
'Left-primary_visual_cortex_monocular_area': 'Left-primary_visual_cortex_monocular_area',
'Left-rostral_amygdalopiriform_area': 'Left-rostral_amygdalopiriform_area',
'Left-s_lu': 'Left-s_lu',
'Left-secondary_auditory_cortex_dorsal_area': 'Left-secondary_auditory_cortex_dorsal_area',
'Left-secondary_auditory_cortex_ventral_area': 'Left-secondary_auditory_cortex_ventral_area',
'Left-secondary_motor_cortex': 'Left-secondary_motor_cortex',
'Left-secondary_somatosensory_cortex': 'Left-secondary_somatosensory_cortex',
'Left-secondary_visual_cortex_lateral_area': 'Left-secondary_visual_cortex_lateral_area',
'Left-secondary_visual_cortex_mediolateral_area': 'Left-secondary_visual_cortex_mediolateral_area',
'Left-secondary_visual_cortex_mediomedial_area': 'Left-secondary_visual_cortex_mediomedial_area',
'Left-simple_lobule_lobule_6': 'Left-simple_lobule_lobule_6',
'Left-simple_lobule_white_matter': 'Left-simple_lobule_white_matter',
'Left-stria_medullaris': 'Left-stria_medullaris',
'Left-stria_terminalis': 'Left-stria_terminalis',
'Left-striatum': 'Left-striatum',
'Left-subependymale_zone_rhinocele': 'Left-subependymale_zone_rhinocele',
'Left-subiculum': 'Left-subiculum',
'Left-superior_olivary_complex': 'Left-superior_olivary_complex',
'Left-temporal_association_area': 'Left-temporal_association_area',
'Left-thalamus': 'Left-thalamus',
'Left-trunk_of_crus_2_and_paramedian_white_matter': 'Left-trunk_of_crus_2_and_paramedian_white_matter',
'Left-trunk_of_simple_and_crus_1_white_matter': 'Left-trunk_of_simple_and_crus_1_white_matter',
'Left-ventral_intermediate_entorhinal_cortex': 'Left-ventral_intermediate_entorhinal_cortex',
'Left-ventral_nucleus_of_the_endopiriform_claustrum': 'Left-ventral_nucleus_of_the_endopiriform_claustrum',
'Left-ventral_orbital_cortex': 'Left-ventral_orbital_cortex',
'Left-ventral_tenia_tecta': 'Left-ventral_tenia_tecta',
'Right-accessory_olfactory_bulb_glomerular_external_plexiform_and_mitral_cell_layer': 'Right-accessory_olfactory_bulb_glomerular_external_plexiform_and_mitral_cell_layer',
'Right-accessory_olfactory_bulb_granule_cell_layer': 'Right-accessory_olfactory_bulb_granule_cell_layer',
'Right-amygdala': 'Right-amygdala',
'Right-amygdalopiriform_transition_area': 'Right-amygdalopiriform_transition_area',
'Right-anterior_commissure_pars_anterior': 'Right-anterior_commissure_pars_anterior',
'Right-anterior_commissure_pars_posterior': 'Right-anterior_commissure_pars_posterior',
'Right-anterior_lobule_lobules_4_5': 'Right-anterior_lobule_lobules_4_5',
'Right-anterior_lobule_white_matter': 'Right-anterior_lobule_white_matter',
'Right-anterior_olfactory_nucleus': 'Right-anterior_olfactory_nucleus',
'Right-basal_forebrain': 'Right-basal_forebrain',
'Right-bed_nucleus_of_stria_terminalis': 'Right-bed_nucleus_of_stria_terminalis',
'Right-ca10r': 'Right-ca10r',
'Right-ca1py': 'Right-ca1py',
'Right-ca1rad': 'Right-ca1rad',
'Right-ca20r': 'Right-ca20r',
'Right-ca2py': 'Right-ca2py',
'Right-ca2rad': 'Right-ca2rad',
'Right-ca30r': 'Right-ca30r',
'Right-ca3py_inner': 'Right-ca3py_inner',
'Right-ca3py_outer': 'Right-ca3py_outer',
'Right-ca3rad': 'Right-ca3rad',
'Right-caudomedial_entorhinal_cortex': 'Right-caudomedial_entorhinal_cortex',
'Right-cerebellar_peduncle_inferior': 'Right-cerebellar_peduncle_inferior',
'Right-cerebellar_peduncle_middle': 'Right-cerebellar_peduncle_middle',
'Right-cerebellar_peduncle_superior': 'Right-cerebellar_peduncle_superior',
'Right-cerebral_peduncle': 'Right-cerebral_peduncle',
'Right-cingulate_cortex_area_24a': 'Right-cingulate_cortex_area_24a',
'Right-cingulate_cortex_area_24a_2': 'Right-cingulate_cortex_area_24a_2',
'Right-cingulate_cortex_area_24b': 'Right-cingulate_cortex_area_24b',
'Right-cingulate_cortex_area_24b_2': 'Right-cingulate_cortex_area_24b_2',
'Right-cingulate_cortex_area_25': 'Right-cingulate_cortex_area_25',
'Right-cingulate_cortex_area_29a': 'Right-cingulate_cortex_area_29a',
'Right-cingulate_cortex_area_29b': 'Right-cingulate_cortex_area_29b',
'Right-cingulate_cortex_area_29c': 'Right-cingulate_cortex_area_29c',
'Right-cingulate_cortex_area_30': 'Right-cingulate_cortex_area_30',
'Right-cingulate_cortex_area_32': 'Right-cingulate_cortex_area_32',
'Right-cingulum': 'Right-cingulum',
'Right-claustrum': 'Right-claustrum',
'Right-claustrum_dorsal_part': 'Right-claustrum_dorsal_part',
'Right-claustrum_ventral_part': 'Right-claustrum_ventral_part',
'Right-colliculus_inferior': 'Right-colliculus_inferior',
'Right-colliculus_superior': 'Right-colliculus_superior',
'Right-copula_pyramis_lobule_8': 'Right-copula_pyramis_lobule_8',
'Right-copula_white_matter': 'Right-copula_white_matter',
'Right-corpus_callosum': 'Right-corpus_callosum',
'Right-cortex_amygdala_transition_zones': 'Right-cortex_amygdala_transition_zones',
'Right-corticospinal_tract_pyramids': 'Right-corticospinal_tract_pyramids',
'Right-crus_1_ansiform_lobule_lobule_6': 'Right-crus_1_ansiform_lobule_lobule_6',
'Right-crus_1_white_matter': 'Right-crus_1_white_matter',
'Right-crus_2_ansiform_lobule_lobule_7': 'Right-crus_2_ansiform_lobule_lobule_7',
'Right-crus_2_white_matter': 'Right-crus_2_white_matter',
'Right-cuneate_nucleus': 'Right-cuneate_nucleus',
'Right-dentate_nucleus': 'Right-dentate_nucleus',
'Right-dorsal_intermediate_entorhinal_cortex': 'Right-dorsal_intermediate_entorhinal_cortex',
'Right-dorsal_nucleus_of_the_endopiriform': 'Right-dorsal_nucleus_of_the_endopiriform',
'Right-dorsal_tenia_tecta': 'Right-dorsal_tenia_tecta',
'Right-dorsolateral_entorhinal_cortex': 'Right-dorsolateral_entorhinal_cortex',
'Right-dorsolateral_orbital_cortex': 'Right-dorsolateral_orbital_cortex',
'Right-ectorhinal_cortex': 'Right-ectorhinal_cortex',
'Right-facial_nerve_cranial_nerve_7': 'Right-facial_nerve_cranial_nerve_7',
'Right-fasciculus_retroflexus': 'Right-fasciculus_retroflexus',
'Right-fastigial_nucleus': 'Right-fastigial_nucleus',
'Right-fimbria': 'Right-fimbria',
'Right-flocculus_fl': 'Right-flocculus_fl',
'Right-flocculus_white_matter': 'Right-flocculus_white_matter',
'Right-fornix': 'Right-fornix',
'Right-frontal_association_cortex': 'Right-frontal_association_cortex',
'Right-frontal_cortex_area_3': 'Right-frontal_cortex_area_3',
'Right-fundus_of_striatum': 'Right-fundus_of_striatum',
'Right-globus_pallidus': 'Right-globus_pallidus',
'Right-gr_dg': 'Right-gr_dg',
'Right-habenular_commissure': 'Right-habenular_commissure',
'Right-hypothalamus': 'Right-hypothalamus',
'Right-inferior_olivary_complex': 'Right-inferior_olivary_complex',
'Right-insular_region_not_subdivided': 'Right-insular_region_not_subdivided',
'Right-intermediate_nucleus_of_the_endopiriform_claustrum': 'Right-intermediate_nucleus_of_the_endopiriform_claustrum',
'Right-internal_capsule': 'Right-internal_capsule',
'Right-l_mol': 'Right-l_mol',
'Right-lateral_olfactory_tract': 'Right-lateral_olfactory_tract',
'Right-lateral_orbital_cortex': 'Right-lateral_orbital_cortex',
'Right-lateral_parietal_association_cortex': 'Right-lateral_parietal_association_cortex',
'Right-lateral_septum': 'Right-lateral_septum',
'Right-lateral_ventricle': 'Right-lateral_ventricle',
'Right-mammillary_bodies': 'Right-mammillary_bodies',
'Right-mammilothalamic_tract': 'Right-mammilothalamic_tract',
'Right-medial_amygdala': 'Right-medial_amygdala',
'Right-medial_entorhinal_cortex': 'Right-medial_entorhinal_cortex',
'Right-medial_lemniscus_medial_longitudinal_fasciculus': 'Right-medial_lemniscus_medial_longitudinal_fasciculus',
'Right-medial_orbital_cortex': 'Right-medial_orbital_cortex',
'Right-medial_parietal_association_cortex': 'Right-medial_parietal_association_cortex',
'Right-medial_preoptic_nucleus': 'Right-medial_preoptic_nucleus',
'Right-medial_septum': 'Right-medial_septum',
'Right-mo_dg_Right': 'Right-mo_dg_Right',
'Right-nucleus_accumbens': 'Right-nucleus_accumbens',
'Right-nucleus_interpositus': 'Right-nucleus_interpositus',
'Right-olfactory_bulb_external_plexiform_layer': 'Right-olfactory_bulb_external_plexiform_layer',
'Right-olfactory_bulb_glomerular_layer': 'Right-olfactory_bulb_glomerular_layer',
'Right-olfactory_bulb_granule_cell_layer': 'Right-olfactory_bulb_granule_cell_layer',
'Right-olfactory_bulb_internal_plexiform_layer': 'Right-olfactory_bulb_internal_plexiform_layer',
'Right-olfactory_bulb_mitral_cell_layer': 'Right-olfactory_bulb_mitral_cell_layer',
'Right-olfactory_peduncle': 'Right-olfactory_peduncle',
'Right-olfactory_tubercle': 'Right-olfactory_tubercle',
'Right-optic_tract': 'Right-optic_tract',
'Right-paraflocculus_pfl': 'Right-paraflocculus_pfl',
'Right-paraflocculus_white_matter': 'Right-paraflocculus_white_matter',
'Right-paramedian_lobule': 'Right-paramedian_lobule',
'Right-paramedian_lobule_lobule_7': 'Right-paramedian_lobule_lobule_7',
'Right-parietal_cortex_posterior_area_rostral_part': 'Right-parietal_cortex_posterior_area_rostral_part',
'Right-perirhinal_cortex': 'Right-perirhinal_cortex',
'Right-piriform_cortex': 'Right-piriform_cortex',
'Right-po_dg': 'Right-po_dg',
'Right-pontine_nucleus': 'Right-pontine_nucleus',
'Right-posterolateral_cortical_amygdaloid_area': 'Right-posterolateral_cortical_amygdaloid_area',
'Right-posteromedial_cortical_amygdaloid_area': 'Right-posteromedial_cortical_amygdaloid_area',
'Right-pre_para_subiculum': 'Right-pre_para_subiculum',
'Right-primary_auditory_cortex': 'Right-primary_auditory_cortex',
'Right-primary_motor_cortex': 'Right-primary_motor_cortex',
'Right-primary_somatosensory_cortex': 'Right-primary_somatosensory_cortex',
'Right-primary_somatosensory_cortex_barrel_field': 'Right-primary_somatosensory_cortex_barrel_field',
'Right-primary_somatosensory_cortex_dysgranular_zone': 'Right-primary_somatosensory_cortex_dysgranular_zone',
'Right-primary_somatosensory_cortex_forelimb_region': 'Right-primary_somatosensory_cortex_forelimb_region',
'Right-primary_somatosensory_cortex_hindlimb_region': 'Right-primary_somatosensory_cortex_hindlimb_region',
'Right-primary_somatosensory_cortex_jaw_region': 'Right-primary_somatosensory_cortex_jaw_region',
'Right-primary_somatosensory_cortex_shoulder_region': 'Right-primary_somatosensory_cortex_shoulder_region',
'Right-primary_somatosensory_cortex_trunk_region': 'Right-primary_somatosensory_cortex_trunk_region',
'Right-primary_somatosensory_cortex_upper_lip_region': 'Right-primary_somatosensory_cortex_upper_lip_region',
'Right-primary_visual_cortex': 'Right-primary_visual_cortex',
'Right-primary_visual_cortex_binocular_area': 'Right-primary_visual_cortex_binocular_area',
'Right-primary_visual_cortex_monocular_area': 'Right-primary_visual_cortex_monocular_area',
'Right-rostral_amygdalopiriform_area': 'Right-rostral_amygdalopiriform_area',
'Right-s_lu': 'Right-s_lu',
'Right-secondary_auditory_cortex_dorsal_area': 'Right-secondary_auditory_cortex_dorsal_area',
'Right-secondary_auditory_cortex_ventral_area': 'Right-secondary_auditory_cortex_ventral_area',
'Right-secondary_motor_cortex': 'Right-secondary_motor_cortex',
'Right-secondary_somatosensory_cortex': 'Right-secondary_somatosensory_cortex',
'Right-secondary_visual_cortex_lateral_area': 'Right-secondary_visual_cortex_lateral_area',
'Right-secondary_visual_cortex_mediolateral_area': 'Right-secondary_visual_cortex_mediolateral_area',
'Right-secondary_visual_cortex_mediomedial_area': 'Right-secondary_visual_cortex_mediomedial_area',
'Right-simple_lobule_lobule_6': 'Right-simple_lobule_lobule_6',
'Right-simple_lobule_white_matter': 'Right-simple_lobule_white_matter',
'Right-stria_medullaris': 'Right-stria_medullaris',
'Right-stria_terminalis': 'Right-stria_terminalis',
'Right-striatum': 'Right-striatum',
'Right-subependymale_zone_rhinocele': 'Right-subependymale_zone_rhinocele',
'Right-subiculum': 'Right-subiculum',
'Right-superior_olivary_complex': 'Right-superior_olivary_complex',
'Right-temporal_association_area': 'Right-temporal_association_area',
'Right-thalamus': 'Right-thalamus',
'Right-trunk_of_crus_2_and_paramedian_white_matter': 'Right-trunk_of_crus_2_and_paramedian_white_matter',
'Right-trunk_of_simple_and_crus_1_white_matter': 'Right-trunk_of_simple_and_crus_1_white_matter',
'Right-ventral_intermediate_entorhinal_cortex': 'Right-ventral_intermediate_entorhinal_cortex',
'Right-ventral_nucleus_of_the_endopiriform_claustrum': 'Right-ventral_nucleus_of_the_endopiriform_claustrum',
'Right-ventral_orbital_cortex': 'Right-ventral_orbital_cortex',
'Right-ventral_tenia_tecta': 'Right-ventral_tenia_tecta',
}
# Dorr areas for mouse atlas
cortAreasIndexMapDorr = {
'Left-amygdala': 'Left-amygdala',
'Left-anterior_commissure_pars_anterior': 'Left-anterior_commissure_pars_anterior',
'Left-anterior_commissure_pars_posterior': 'Left-anterior_commissure_pars_posterior',
'Left-arbor_vita_of_cerebellum': 'Left-arbor_vita_of_cerebellum',
'Left-basal_forebrain': 'Left-basal_forebrain',
'Left-bed_nucleus_of_stria_terminalis': 'Left-bed_nucleus_of_stria_terminalis',
'Left-cerebellar_cortex': 'Left-cerebellar_cortex',
'Left-cerebellar_peduncle_inferior': 'Left-cerebellar_peduncle_inferior',
'Left-cerebellar_peduncle_middle': 'Left-cerebellar_peduncle_middle',
'Left-cerebellar_peduncle_superior': 'Left-cerebellar_peduncle_superior',
'Left-cerebral_cortex_entorhinal_cortex': 'Left-cerebral_cortex_entorhinal_cortex',
'Left-cerebral_cortex_frontal_lobe': 'Left-cerebral_cortex_frontal_lobe',
'Left-cerebral_cortex_occipital_lobe': 'Left-cerebral_cortex_occipital_lobe',
'Left-cerebral_cortex_parieto_temporal_lobe': 'Left-cerebral_cortex_parieto_temporal_lobe',
'Left-cerebral_peduncle': 'Left-cerebral_peduncle',
'Left-colliculus_inferior': 'Left-colliculus_inferior',
'Left-colliculus_superior': 'Left-colliculus_superior',
'Left-corpus_callosum': 'Left-corpus_callosum',
'Left-corticospinal_tract_pyramids': 'Left-corticospinal_tract_pyramids',
'Left-cuneate_nucleus': 'Left-cuneate_nucleus',
'Left-dentate_gyrus_of_hippocampus': 'Left-dentate_gyrus_of_hippocampus',
'Left-facial_nerve_cranial_nerve_7': 'Left-facial_nerve_cranial_nerve_7',
'Left-fasciculus_retroflexus': 'Left-fasciculus_retroflexus',
'Left-fimbria': 'Left-fimbria',
'Left-fornix': 'Left-fornix',
'Left-fundus_of_striatum': 'Left-fundus_of_striatum',
'Left-globus_pallidus': 'Left-globus_pallidus',
'Left-habenular_commissure': 'Left-habenular_commissure',
'Left-hippocampus': 'Left-hippocampus',
'Left-hypothalamus': 'Left-hypothalamus',
'Left-inferior_olivary_complex': 'Left-inferior_olivary_complex',
'Left-internal_capsule': 'Left-internal_capsule',
'Left-lateral_olfactory_tract': 'Left-lateral_olfactory_tract',
'Left-lateral_septum': 'Left-lateral_septum',
'Left-lateral_ventricle': 'Left-lateral_ventricle',
'Left-mammillary_bodies': 'Left-mammillary_bodies',
'Left-mammilothalamic_tract': 'Left-mammilothalamic_tract',
'Left-medial_lemniscus_medial_longitudinal_fasciculus': 'Left-medial_lemniscus_medial_longitudinal_fasciculus',
'Left-medial_septum': 'Left-medial_septum',
'Left-nucleus_accumbens': 'Left-nucleus_accumbens',
'Left-olfactory_bulbs': 'Left-olfactory_bulbs',
'Left-olfactory_tubercle': 'Left-olfactory_tubercle',
'Left-optic_tract': 'Left-optic_tract',
'Left-pontine_nucleus': 'Left-pontine_nucleus',
'Left-pre_para_subiculum': 'Left-pre_para_subiculum',
'Left-stratum_granulosum_of_hippocampus': 'Left-stratum_granulosum_of_hippocampus',
'Left-stria_medullaris': 'Left-stria_medullaris',
'Left-stria_terminalis': 'Left-stria_terminalis',
'Left-striatum': 'Left-striatum',
'Left-subependymale_zone_rhinocele': 'Left-subependymale_zone_rhinocele',
'Left-superior_olivary_complex': 'Left-superior_olivary_complex',
'Left-thalamus': 'Left-thalamus',
'Right-amygdala': 'Right-amygdala',
'Right-anterior_commissure_pars_anterior': 'Right-anterior_commissure_pars_anterior',
'Right-anterior_commissure_pars_posterior': 'Right-anterior_commissure_pars_posterior',
'Right-arbor_vita_of_cerebellum': 'Right-arbor_vita_of_cerebellum',
'Right-basal_forebrain': 'Right-basal_forebrain',
'Right-bed_nucleus_of_stria_terminalis': 'Right-bed_nucleus_of_stria_terminalis',
'Right-cerebellar_cortex': 'Right-cerebellar_cortex',
'Right-cerebellar_peduncle_inferior': 'Right-cerebellar_peduncle_inferior',
'Right-cerebellar_peduncle_middle': 'Right-cerebellar_peduncle_middle',
'Right-cerebellar_peduncle_superior': 'Right-cerebellar_peduncle_superior',
'Right-cerebral_cortex_entorhinal_cortex': 'Right-cerebral_cortex_entorhinal_cortex',
'Right-cerebral_cortex_frontal_lobe': 'Right-cerebral_cortex_frontal_lobe',
'Right-cerebral_cortex_occipital_lobe': 'Right-cerebral_cortex_occipital_lobe',
'Right-cerebral_cortex_parieto_temporal_lobe': 'Right-cerebral_cortex_parieto_temporal_lobe',
'Right-cerebral_peduncle': 'Right-cerebral_peduncle',
'Right-colliculus_inferior': 'Right-colliculus_inferior',
'Right-colliculus_superior': 'Right-colliculus_superior',
'Right-corpus_callosum': 'Right-corpus_callosum',
'Right-corticospinal_tract_pyramids': 'Right-corticospinal_tract_pyramids',
'Right-cuneate_nucleus': 'Right-cuneate_nucleus',
'Right-dentate_gyrus_of_hippocampus': 'Right-dentate_gyrus_of_hippocampus',
'Right-facial_nerve_cranial_nerve_7': 'Right-facial_nerve_cranial_nerve_7',
'Right-fasciculus_retroflexus': 'Right-fasciculus_retroflexus',
'Right-fimbria': 'Right-fimbria',
'Right-fornix': 'Right-fornix',
'Right-fundus_of_striatum': 'Right-fundus_of_striatum',
'Right-globus_pallidus': 'Right-globus_pallidus',
'Right-habenular_commissure': 'Right-habenular_commissure',
'Right-hippocampus': 'Right-hippocampus',
'Right-hypothalamus': 'Right-hypothalamus',
'Right-inferior_olivary_complex': 'Right-inferior_olivary_complex',
'Right-internal_capsule': 'Right-internal_capsule',
'Right-lateral_olfactory_tract': 'Right-lateral_olfactory_tract',
'Right-lateral_septum': 'Right-lateral_septum',
'Right-lateral_ventricle': 'Right-lateral_ventricle',
'Right-mammillary_bodies': 'Right-mammillary_bodies',
'Right-mammilothalamic_tract': 'Right-mammilothalamic_tract',
'Right-medial_lemniscus_medial_longitudinal_fasciculus': 'Right-medial_lemniscus_medial_longitudinal_fasciculus',
'Right-medial_septum': 'Right-medial_septum',
'Right-nucleus_accumbens': 'Right-nucleus_accumbens',
'Right-olfactory_bulbs': 'Right-olfactory_bulbs',
'Right-olfactory_tubercle': 'Right-olfactory_tubercle',
'Right-optic_tract': 'Right-optic_tract',
'Right-pontine_nucleus': 'Right-pontine_nucleus',
'Right-pre_para_subiculum': 'Right-pre_para_subiculum',
'Right-stratum_granulosum_of_hippocampus': 'Right-stratum_granulosum_of_hippocampus',
'Right-stria_medullaris': 'Right-stria_medullaris',
'Right-stria_terminalis': 'Right-stria_terminalis',
'Right-striatum': 'Right-striatum',
'Right-subependymale_zone_rhinocele': 'Right-subependymale_zone_rhinocele',
'Right-superior_olivary_complex': 'Right-superior_olivary_complex',
'Right-thalamus': 'Right-thalamus',
}
### Tourville atlas ###
# Left-Hand-Side = Blender Regions Right-Hand-Side = Regions in custom input atlas (.csv INPUT_FILE)
cortAreasIndexMapTourville = {
'Right-caudalanteriorcingulate': 'Right-caudalanteriorcingulate',
'Right-caudalmiddlefrontal': 'Right-caudalmiddlefrontal',
'Right-cuneus': 'Right-cuneus',
'Right-entorhinal': 'Right-entorhinal',
'Right-fusiform': 'Right-fusiform',
'Right-inferiorparietal': 'Right-inferiorparietal',
'Right-inferiortemporal': 'Right-inferiortemporal',
'Right-insula': 'Right-insula',
'Right-isthmuscingulate': 'Right-isthmuscingulate',
'Right-lateraloccipital': 'Right-lateraloccipital',
'Right-lateralorbitofrontal': 'Right-lateralorbitofrontal',
'Right-lingual': 'Right-lingual',
'Right-medialorbitofrontal': 'Right-medialorbitofrontal',
'Right-middletemporal': 'Right-middletemporal',
'Right-paracentral': 'Right-paracentral',
'Right-parahippocampal': 'Right-parahippocampal',
'Right-parsopercularis': 'Right-parsopercularis',
'Right-parsorbitalis': 'Right-parsorbitalis',
'Right-parstriangularis': 'Right-parstriangularis',
'Right-pericalcarine': 'Right-pericalcarine',
'Right-postcentral': 'Right-postcentral',
'Right-posteriorcingulate': 'Right-posteriorcingulate',
'Right-precentral': 'Right-precentral',
'Right-precuneus': 'Right-precuneus',
'Right-rostralanteriorcingulate': 'Right-rostralanteriorcingulate',
'Right-rostralmiddlefrontal': 'Right-rostralmiddlefrontal',
'Right-superiorfrontal': 'Right-superiorfrontal',
'Right-superiorparietal': 'Right-superiorparietal',
'Right-superiortemporal': 'Right-superiortemporal',
'Right-supramarginal': 'Right-supramarginal',
'Right-transversetemporal': 'Right-transversetemporal',
'Right-unknown':-1, # this is actually the middle region inside the cortical surface. color it as gray
'Left-caudalanteriorcingulate': 'Left-caudalanteriorcingulate',
'Left-caudalmiddlefrontal': 'Left-caudalmiddlefrontal',
'Left-cuneus': 'Left-cuneus',
'Left-entorhinal': 'Left-entorhinal',
'Left-fusiform': 'Left-fusiform',
'Left-inferiorparietal': 'Left-inferiorparietal',
'Left-inferiortemporal': 'Left-inferiortemporal',
'Left-insula': 'Left-insula',
'Left-isthmuscingulate': 'Left-isthmuscingulate',
'Left-lateraloccipital': 'Left-lateraloccipital',
'Left-lateralorbitofrontal': 'Left-lateralorbitofrontal',
'Left-lingual': 'Left-lingual',
'Left-medialorbitofrontal': 'Left-medialorbitofrontal',
'Left-middletemporal': 'Left-middletemporal',
'Left-paracentral': 'Left-paracentral',
'Left-parahippocampal': 'Left-parahippocampal',
'Left-parsopercularis': 'Left-parsopercularis',
'Left-parsorbitalis': 'Left-parsorbitalis',
'Left-parstriangularis': 'Left-parstriangularis',
'Left-pericalcarine': 'Left-pericalcarine',
'Left-postcentral': 'Left-postcentral',
'Left-posteriorcingulate': 'Left-posteriorcingulate',
'Left-precentral': 'Left-precentral',
'Left-precuneus': 'Left-precuneus',
'Left-rostralanteriorcingulate': 'Left-rostralanteriorcingulate',
'Left-rostralmiddlefrontal': 'Left-rostralmiddlefrontal',
'Left-superiorfrontal': 'Left-superiorfrontal',
'Left-superiorparietal': 'Left-superiorparietal',
'Left-superiortemporal': 'Left-superiortemporal',
'Left-supramarginal': 'Left-supramarginal',
'Left-transversetemporal': 'Left-transversetemporal',
'Left-unknown':-1 # this is actually the middle region inside the cortical surface. color it as gray
}
### For Custom ATLAS #####
# MAP from custom atlas to DK. Left-Hand-Side = Blender Regions Right-Hand-Side = Regions in custom input atlas (.csv INPUT_FILE)
cortAreasIndexMapCustom = {
'Right-bankssts':-1, # -1 means do not colour this region
'Right-caudalanteriorcingulate':'Right-anterior cingulate',
'Right-caudalmiddlefrontal':'Right-medial frontal',
'Right-cuneus':'Right-cuneus',
'Right-entorhinal':'Right-entorhinal',
'Right-frontalpole':'Right-frontal pole',
'Right-fusiform':'Right-fusiform',
'Right-inferiorparietal':'Right-angular',
'Right-inferiortemporal':'Right-inferior temporal',
'Right-insula':'Right-anterior insula',
'Right-isthmuscingulate':'Right-posterior cingulate',
'Right-lateraloccipital':'Right-inferior occipital',
'Right-lateralorbitofrontal':'Right-medial frontal',
'Right-lingual':'Right-lingual',
'Right-medialorbitofrontal':'Right-medial frontal',
'Right-middletemporal':'Right-middle temporal',
'Right-paracentral':'Right-precentral',
'Right-parahippocampal':'Right-parahippocampal',
'Right-parsopercularis':'Right-central operculum',
'Right-parsorbitalis':'Right-anterior orbital',
'Right-parstriangularis':'Right-angular',
'Right-pericalcarine':'Right-calcarine',
'Right-postcentral':'Right-postcentral',
'Right-posteriorcingulate':'Right-posterior cingulate',
'Right-precentral':'Right-precentral',
'Right-precuneus':'Right-precuneus',
'Right-rostralanteriorcingulate':'Right-anterior cingulate',
'Right-rostralmiddlefrontal':'Right-middle frontal',
'Right-superiorfrontal':'Right-superior frontal',
'Right-superiorparietal':'Right-superior parietal',
'Right-superiortemporal':'Right-superior temporal',
'Right-supramarginal':'Right-supramarginal',
'Right-temporalpole':'Right-temporal pole',
'Right-transversetemporal':'Right-planum temporale',
'Right-unknown':-1, # this is actually the middle region inside the cortical surface. color it as gray
'Left-bankssts':-1, # -1 means do not colour this region
'Left-caudalanteriorcingulate':'Left-anterior cingulate',
'Left-caudalmiddlefrontal':'Left-medial frontal',
'Left-cuneus':'Left-cuneus',
'Left-entorhinal':'Left-entorhinal',
'Left-frontalpole':'Left-frontal pole',
'Left-fusiform':'Left-fusiform',
'Left-inferiorparietal':'Left-angular',
'Left-inferiortemporal':'Left-inferior temporal',
'Left-insula':'Left-anterior insula',
'Left-isthmuscingulate':'Left-posterior cingulate',
'Left-lateraloccipital':'Left-inferior occipital',
'Left-lateralorbitofrontal':'Left-medial frontal',
'Left-lingual':'Left-lingual',
'Left-medialorbitofrontal':'Left-medial frontal',
'Left-middletemporal':'Left-middle temporal',
'Left-paracentral':'Left-precentral',
'Left-parahippocampal':'Left-parahippocampal',
'Left-parsopercularis':'Left-central operculum',
'Left-parsorbitalis':'Left-anterior orbital',
'Left-parstriangularis':'Left-angular',
'Left-pericalcarine':'Left-calcarine',
'Left-postcentral':'Left-postcentral',
'Left-posteriorcingulate':'Left-posterior cingulate',
'Left-precentral':'Left-precentral',
'Left-precuneus':'Left-precuneus',
'Left-rostralanteriorcingulate':'Left-anterior cingulate',
'Left-rostralmiddlefrontal':'Left-middle frontal',
'Left-superiorfrontal':'Left-superior frontal',
'Left-superiorparietal':'Left-superior parietal',
'Left-superiortemporal':'Left-superior temporal',
'Left-supramarginal':'Left-supramarginal',
'Left-temporalpole':'Left-temporal pole',
'Left-transversetemporal':'Left-planum temporale',
'Left-unknown':-1 # this is actually the middle region inside the cortical surface. color it as gray
}
# Subcortical areas
# this map is used by all atlases (DK, Destrieux, Tourville)
subcortAreasIndexMap = {
'Left-Accumbens-area': 'Left-Accumbens-area', # -1 means do not colour this region
'Left-Caudate': 'Left-Caudate',
'Left-Cerebellum-White-Matter': 'Left-Cerebellum-White-Matter',
'Left-Inf-Lat-Vent': 'Left-Inf-Lat-Vent',
'Left-Pallidum': 'Left-Pallidum',
'Left-Thalamus-Proper': 'Left-Thalamus-Proper',
'Left-Amygdala': 'Left-Amygdala',
'Left-Cerebellum-Cortex': 'Left-Cerebellum-Cortex',
'Left-Hippocampus': 'Left-Hippocampus',
'Left-Lateral-Ventricle': 'Left-Lateral-Ventricle',
'Left-Putamen': 'Left-Putamen',
'Left-VentralDC': 'Left-VentralDC',
'Right-Accumbens-area': 'Right-Accumbens-area', # -1 means do not colour this region
'Right-Caudate': 'Right-Caudate',
'Right-Cerebellum-White-Matter': 'Right-Cerebellum-White-Matter',
'Right-Inf-Lat-Vent': 'Right-Inf-Lat-Vent',
'Right-Pallidum': 'Right-Pallidum',
'Right-Thalamus-Proper': 'Right-Thalamus-Proper',
'Right-Amygdala': 'Right-Amygdala',
'Right-Cerebellum-Cortex': 'Right-Cerebellum-Cortex',
'Right-Hippocampus': 'Right-Hippocampus',
'Right-Lateral-Ventricle': 'Right-Lateral-Ventricle',