labelconvert LUTs for Schaefer parcellations

share/mrtrix3/labelconvert/Schaefer2018_100Parcels_17Networks_FreeSurferSGM.txt

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+# Default configuration file for MRtrix command labelconfig
+# Extracts the relevant cortical grey matter parcellations from the Schaefer2018 atlas
+# and relevant subcortical grey matter parcellations from the default FreeSurfer segmentation 
+# (desikan_killiany)
+
+# As of 07/2023 the left accumbens area is incorrectly labeled
+# as "Left-Accumbens-a" instead of "Left-Accumbens-area"
+# in the official Schaefer2018 LUTs
+# (see https://github.com/ThomasYeoLab/CBIG/issues/49).
+# Since labelconvert uses string recognition,
+# we provide both strings ("Left-Accumbens-a"/"Left-Accumbens-area")
+# and match them with label 58.
+# The second label can be omitted should the issue be resolved in the future. 
+
+58 Left-Accumbens-a
+
+0 Unknown
+
+1 17Networks_LH_VisCent_ExStr_1
+2 17Networks_LH_VisCent_ExStr_2
+3 17Networks_LH_VisCent_Striate_1
+4 17Networks_LH_VisCent_ExStr_3
+5 17Networks_LH_VisPeri_ExStrInf_1
+6 17Networks_LH_VisPeri_StriCal_1
+7 17Networks_LH_VisPeri_ExStrSup_1
+8 17Networks_LH_SomMotA_1
+9 17Networks_LH_SomMotA_2
+10 17Networks_LH_SomMotB_Aud_1
+11 17Networks_LH_SomMotB_S2_1
+12 17Networks_LH_SomMotB_S2_2
+13 17Networks_LH_SomMotB_Cent_1
+14 17Networks_LH_DorsAttnA_TempOcc_1
+15 17Networks_LH_DorsAttnA_ParOcc_1
+16 17Networks_LH_DorsAttnA_SPL_1
+17 17Networks_LH_DorsAttnB_PostC_1
+18 17Networks_LH_DorsAttnB_PostC_2
+19 17Networks_LH_DorsAttnB_PostC_3
+20 17Networks_LH_DorsAttnB_FEF_1
+21 17Networks_LH_SalVentAttnA_ParOper_1
+22 17Networks_LH_SalVentAttnA_Ins_1
+23 17Networks_LH_SalVentAttnA_Ins_2
+24 17Networks_LH_SalVentAttnA_ParMed_1
+25 17Networks_LH_SalVentAttnA_FrMed_1
+26 17Networks_LH_SalVentAttnB_PFCl_1
+27 17Networks_LH_SalVentAttnB_PFCmp_1
+28 17Networks_LH_LimbicB_OFC_1
+29 17Networks_LH_LimbicA_TempPole_1
+30 17Networks_LH_LimbicA_TempPole_2
+31 17Networks_LH_ContA_IPS_1
+32 17Networks_LH_ContA_PFCl_1
+33 17Networks_LH_ContA_PFCl_2
+34 17Networks_LH_ContB_PFClv_1
+35 17Networks_LH_ContC_pCun_1
+36 17Networks_LH_ContC_pCun_2
+37 17Networks_LH_ContC_Cingp_1
+38 17Networks_LH_DefaultA_PFCd_1
+39 17Networks_LH_DefaultA_pCunPCC_1
+40 17Networks_LH_DefaultA_PFCm_1
+41 17Networks_LH_DefaultB_Temp_1
+42 17Networks_LH_DefaultB_Temp_2
+43 17Networks_LH_DefaultB_IPL_1
+44 17Networks_LH_DefaultB_PFCd_1
+45 17Networks_LH_DefaultB_PFCl_1
+46 17Networks_LH_DefaultB_PFCv_1
+47 17Networks_LH_DefaultB_PFCv_2
+48 17Networks_LH_DefaultC_Rsp_1
+49 17Networks_LH_DefaultC_PHC_1
+50 17Networks_LH_TempPar_1
+
+51 Left-Cerebellum-Cortex
+
+52 Left-Thalamus-Proper
+53 Left-Caudate
+54 Left-Putamen
+55 Left-Pallidum
+56 Left-Hippocampus
+57 Left-Amygdala
+58 Left-Accumbens-area
+
+59 Right-Thalamus-Proper
+60 Right-Caudate
+61 Right-Putamen
+62 Right-Pallidum
+63 Right-Hippocampus
+64 Right-Amygdala
+65 Right-Accumbens-area
+
+66 17Networks_RH_VisCent_ExStr_1
+67 17Networks_RH_VisCent_ExStr_2
+68 17Networks_RH_VisCent_ExStr_3
+69 17Networks_RH_VisPeri_StriCal_1
+70 17Networks_RH_VisPeri_ExStrInf_1
+71 17Networks_RH_VisPeri_ExStrSup_1
+72 17Networks_RH_SomMotA_1
+73 17Networks_RH_SomMotA_2
+74 17Networks_RH_SomMotA_3
+75 17Networks_RH_SomMotA_4
+76 17Networks_RH_SomMotB_Aud_1
+77 17Networks_RH_SomMotB_S2_1
+78 17Networks_RH_SomMotB_S2_2
+79 17Networks_RH_SomMotB_Cent_1
+80 17Networks_RH_DorsAttnA_TempOcc_1
+81 17Networks_RH_DorsAttnA_ParOcc_1
+82 17Networks_RH_DorsAttnA_SPL_1
+83 17Networks_RH_DorsAttnB_PostC_1
+84 17Networks_RH_DorsAttnB_PostC_2
+85 17Networks_RH_DorsAttnB_FEF_1
+86 17Networks_RH_SalVentAttnA_ParOper_1
+87 17Networks_RH_SalVentAttnA_Ins_1
+88 17Networks_RH_SalVentAttnA_ParMed_1
+89 17Networks_RH_SalVentAttnA_FrMed_1
+90 17Networks_RH_SalVentAttnB_IPL_1
+91 17Networks_RH_SalVentAttnB_PFCl_1
+92 17Networks_RH_SalVentAttnB_PFCmp_1
+93 17Networks_RH_LimbicB_OFC_1
+94 17Networks_RH_LimbicA_TempPole_1
+95 17Networks_RH_ContA_IPS_1
+96 17Networks_RH_ContA_PFCl_1
+97 17Networks_RH_ContA_PFCl_2
+98 17Networks_RH_ContB_Temp_1
+99 17Networks_RH_ContB_IPL_1
+100 17Networks_RH_ContB_PFCld_1
+101 17Networks_RH_ContB_PFClv_1
+102 17Networks_RH_ContC_Cingp_1
+103 17Networks_RH_ContC_pCun_1
+104 17Networks_RH_DefaultA_IPL_1
+105 17Networks_RH_DefaultA_PFCd_1
+106 17Networks_RH_DefaultA_pCunPCC_1
+107 17Networks_RH_DefaultA_PFCm_1
+108 17Networks_RH_DefaultB_PFCd_1
+109 17Networks_RH_DefaultB_PFCv_1
+110 17Networks_RH_DefaultB_PFCv_2
+111 17Networks_RH_DefaultC_Rsp_1
+112 17Networks_RH_DefaultC_PHC_1
+113 17Networks_RH_TempPar_1
+114 17Networks_RH_TempPar_2
+115 17Networks_RH_TempPar_3
+
+116 Right-Cerebellum-Cortex
+

share/mrtrix3/labelconvert/Schaefer2018_100Parcels_7Networks_FreeSurferSGM.txt

@@ -0,0 +1,139 @@
+# Default configuration file for MRtrix command labelconfig
+# Extracts the relevant cortical grey matter parcellations from the Schaefer2018 atlas
+# and relevant subcortical grey matter parcellations from the default FreeSurfer segmentation 
+# (desikan_killiany)
+
+# As of 07/2023 the left accumbens area is incorrectly labeled
+# as "Left-Accumbens-a" instead of "Left-Accumbens-area"
+# in the official Schaefer2018 LUTs
+# (see https://github.com/ThomasYeoLab/CBIG/issues/49).
+# Since labelconvert uses string recognition,
+# we provide both strings ("Left-Accumbens-a"/"Left-Accumbens-area")
+# and match them with label 58.
+# The second label can be omitted should the issue be resolved in the future. 
+
+58 Left-Accumbens-a
+
+0 Unknown
+
+1 7Networks_LH_Vis_1
+2 7Networks_LH_Vis_2
+3 7Networks_LH_Vis_3
+4 7Networks_LH_Vis_4
+5 7Networks_LH_Vis_5
+6 7Networks_LH_Vis_6
+7 7Networks_LH_Vis_7
+8 7Networks_LH_Vis_8
+9 7Networks_LH_Vis_9
+10 7Networks_LH_SomMot_1
+11 7Networks_LH_SomMot_2
+12 7Networks_LH_SomMot_3
+13 7Networks_LH_SomMot_4
+14 7Networks_LH_SomMot_5
+15 7Networks_LH_SomMot_6
+16 7Networks_LH_DorsAttn_Post_1
+17 7Networks_LH_DorsAttn_Post_2
+18 7Networks_LH_DorsAttn_Post_3
+19 7Networks_LH_DorsAttn_Post_4
+20 7Networks_LH_DorsAttn_Post_5
+21 7Networks_LH_DorsAttn_Post_6
+22 7Networks_LH_DorsAttn_PrCv_1
+23 7Networks_LH_DorsAttn_FEF_1
+24 7Networks_LH_SalVentAttn_ParOper_1
+25 7Networks_LH_SalVentAttn_FrOperIns_1
+26 7Networks_LH_SalVentAttn_FrOperIns_2
+27 7Networks_LH_SalVentAttn_PFCl_1
+28 7Networks_LH_SalVentAttn_Med_1
+29 7Networks_LH_SalVentAttn_Med_2
+30 7Networks_LH_SalVentAttn_Med_3
+31 7Networks_LH_Limbic_OFC_1
+32 7Networks_LH_Limbic_TempPole_1
+33 7Networks_LH_Limbic_TempPole_2
+34 7Networks_LH_Cont_Par_1
+35 7Networks_LH_Cont_PFCl_1
+36 7Networks_LH_Cont_pCun_1
+37 7Networks_LH_Cont_Cing_1
+38 7Networks_LH_Default_Temp_1
+39 7Networks_LH_Default_Temp_2
+40 7Networks_LH_Default_Par_1
+41 7Networks_LH_Default_Par_2
+42 7Networks_LH_Default_PFC_1
+43 7Networks_LH_Default_PFC_2
+44 7Networks_LH_Default_PFC_3
+45 7Networks_LH_Default_PFC_4
+46 7Networks_LH_Default_PFC_5
+47 7Networks_LH_Default_PFC_6
+48 7Networks_LH_Default_PFC_7
+49 7Networks_LH_Default_pCunPCC_1
+50 7Networks_LH_Default_pCunPCC_2
+
+51 Left-Cerebellum-Cortex
+
+52 Left-Thalamus-Proper
+53 Left-Caudate
+54 Left-Putamen
+55 Left-Pallidum
+56 Left-Hippocampus
+57 Left-Amygdala
+58 Left-Accumbens-area
+
+59 Right-Thalamus-Proper
+60 Right-Caudate
+61 Right-Putamen
+62 Right-Pallidum
+63 Right-Hippocampus
+64 Right-Amygdala
+65 Right-Accumbens-area
+
+66 7Networks_RH_Vis_1
+67 7Networks_RH_Vis_2
+68 7Networks_RH_Vis_3
+69 7Networks_RH_Vis_4
+70 7Networks_RH_Vis_5
+71 7Networks_RH_Vis_6
+72 7Networks_RH_Vis_7
+73 7Networks_RH_Vis_8
+74 7Networks_RH_SomMot_1
+75 7Networks_RH_SomMot_2
+76 7Networks_RH_SomMot_3
+77 7Networks_RH_SomMot_4
+78 7Networks_RH_SomMot_5
+79 7Networks_RH_SomMot_6
+80 7Networks_RH_SomMot_7
+81 7Networks_RH_SomMot_8
+82 7Networks_RH_DorsAttn_Post_1
+83 7Networks_RH_DorsAttn_Post_2
+84 7Networks_RH_DorsAttn_Post_3
+85 7Networks_RH_DorsAttn_Post_4
+86 7Networks_RH_DorsAttn_Post_5
+87 7Networks_RH_DorsAttn_PrCv_1
+88 7Networks_RH_DorsAttn_FEF_1
+89 7Networks_RH_SalVentAttn_TempOccPar_1
+90 7Networks_RH_SalVentAttn_TempOccPar_2
+91 7Networks_RH_SalVentAttn_FrOperIns_1
+92 7Networks_RH_SalVentAttn_Med_1
+93 7Networks_RH_SalVentAttn_Med_2
+94 7Networks_RH_Limbic_OFC_1
+95 7Networks_RH_Limbic_TempPole_1
+96 7Networks_RH_Cont_Par_1
+97 7Networks_RH_Cont_Par_2
+98 7Networks_RH_Cont_PFCl_1
+99 7Networks_RH_Cont_PFCl_2
+100 7Networks_RH_Cont_PFCl_3
+101 7Networks_RH_Cont_PFCl_4
+102 7Networks_RH_Cont_Cing_1
+103 7Networks_RH_Cont_PFCmp_1
+104 7Networks_RH_Cont_pCun_1
+105 7Networks_RH_Default_Par_1
+106 7Networks_RH_Default_Temp_1
+107 7Networks_RH_Default_Temp_2
+108 7Networks_RH_Default_Temp_3
+109 7Networks_RH_Default_PFCv_1
+110 7Networks_RH_Default_PFCv_2
+111 7Networks_RH_Default_PFCdPFCm_1
+112 7Networks_RH_Default_PFCdPFCm_2
+113 7Networks_RH_Default_PFCdPFCm_3
+114 7Networks_RH_Default_pCunPCC_1
+115 7Networks_RH_Default_pCunPCC_2
+
+116 Right-Cerebellum-Cortex