Dear all,
I’ve mapped the annot files of the schaefer2018 atlas from fsaverage to my subject by using mri_surf2surf;
then I mapped the annots onto the volumetric image by using mri_aparc2aseg;
however, the interp values were big and ordered by FreeSurferColorLUT.txt,
so I wondering how to change the original LUTs to a existed schaefer2018 ordered LUTs?
I’ve tried the labelconvert command, but schaefer2018_order.txt doesn’t have same information with FreeSurferColorLUT.txt.
deyu
Hi there, I am no expert on the matter but I managed to get it working a few weeks ago.
Importantly this is for the Schaefer2018_100Parcels scheme.
From the sounds of it you’re on the right track, you just need an ordered .txt LUT. I’m sure the ordered file is out there somewhere I just couldn’t find it so I made my own. I made it by editing the file here: CBIG/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/project_to_individual/Schaefer2018_100Parcels_7Networks_order_LUT.txt at master · ThomasYeoLab/CBIG · GitHub . I deleted the values not needed and it seemed to work.
labelconvert
Schaefer2018_100Parcels_17Networks_order.mif \
Schaefer2018_100Parcels_17Networks_order_LUT_edit.txt
Schaefer2018_100Parcels_17Networks_order.txt \
Schaefer2018_parcels_nocoreg.mif
My Schaefer2018_100Parcels_17Networks_order_LUT_edit.txt file:
#No. Label Name: R G B A
1001 17Networks_LH_VisCent_ExStr_1 120 18 136 0
1002 17Networks_LH_VisCent_ExStr_2 120 18 137 0
1003 17Networks_LH_VisCent_Striate_1 120 18 138 0
1004 17Networks_LH_VisCent_ExStr_3 120 18 139 0
1005 17Networks_LH_VisPeri_ExStrInf_1 255 0 2 0
1006 17Networks_LH_VisPeri_StriCal_1 255 0 3 0
1007 17Networks_LH_VisPeri_ExStrSup_1 255 0 4 0
1008 17Networks_LH_SomMotA_1 70 130 181 0
1009 17Networks_LH_SomMotA_2 70 130 182 0
1010 17Networks_LH_SomMotB_Aud_1 43 204 165 0
1011 17Networks_LH_SomMotB_S2_1 43 204 166 0
1012 17Networks_LH_SomMotB_S2_2 43 204 167 0
1013 17Networks_LH_SomMotB_Cent_1 43 204 168 0
1014 17Networks_LH_DorsAttnA_TempOcc_1 74 156 61 0
1015 17Networks_LH_DorsAttnA_ParOcc_1 74 156 62 0
1016 17Networks_LH_DorsAttnA_SPL_1 74 156 63 0
1017 17Networks_LH_DorsAttnB_PostC_1 0 118 16 0
1018 17Networks_LH_DorsAttnB_PostC_2 0 118 17 0
1019 17Networks_LH_DorsAttnB_PostC_3 0 118 18 0
1020 17Networks_LH_DorsAttnB_FEF_1 0 119 15 0
1021 17Networks_LH_SalVentAttnA_ParOper_1 196 58 251 0
1022 17Networks_LH_SalVentAttnA_Ins_1 196 59 251 0
1023 17Networks_LH_SalVentAttnA_Ins_2 196 59 252 0
1024 17Networks_LH_SalVentAttnA_ParMed_1 196 59 253 0
1025 17Networks_LH_SalVentAttnA_FrMed_1 197 58 251 0
1026 17Networks_LH_SalVentAttnB_PFCl_1 255 153 214 0
1027 17Networks_LH_SalVentAttnB_PFCmp_1 255 151 214 0
1028 17Networks_LH_LimbicB_OFC_1 122 135 51 0
1029 17Networks_LH_LimbicA_TempPole_1 220 248 165 0
1030 17Networks_LH_LimbicA_TempPole_2 220 248 166 0
1031 17Networks_LH_ContA_IPS_1 230 148 36 0
1032 17Networks_LH_ContA_PFCl_1 230 149 36 0
1033 17Networks_LH_ContA_PFCl_2 230 149 37 0
1034 17Networks_LH_ContB_PFClv_1 136 50 75 0
1035 17Networks_LH_ContC_pCun_1 119 140 177 0
1036 17Networks_LH_ContC_pCun_2 119 140 178 0
1037 17Networks_LH_ContC_Cingp_1 119 140 179 0
1038 17Networks_LH_DefaultA_PFCd_1 255 255 2 0
1039 17Networks_LH_DefaultA_pCunPCC_1 255 254 1 0
1040 17Networks_LH_DefaultA_PFCm_1 254 255 1 0
1041 17Networks_LH_DefaultB_Temp_1 205 62 79 0
1042 17Networks_LH_DefaultB_Temp_2 205 62 80 0
1043 17Networks_LH_DefaultB_IPL_1 205 62 81 0
1044 17Networks_LH_DefaultB_PFCd_1 205 63 79 0
1045 17Networks_LH_DefaultB_PFCl_1 205 63 80 0
1046 17Networks_LH_DefaultB_PFCv_1 206 62 79 0
1047 17Networks_LH_DefaultB_PFCv_2 206 62 80 0
1048 17Networks_LH_DefaultC_Rsp_1 0 0 132 0
1049 17Networks_LH_DefaultC_PHC_1 0 1 131 0
1050 17Networks_LH_TempPar_1 9 41 250 0
2001 17Networks_RH_VisCent_ExStr_1 124 19 136 0
2002 17Networks_RH_VisCent_ExStr_2 124 19 137 0
2003 17Networks_RH_VisCent_ExStr_3 124 19 138 0
2004 17Networks_RH_VisPeri_StriCal_1 250 0 2 0
2005 17Networks_RH_VisPeri_ExStrInf_1 250 0 3 0
2006 17Networks_RH_VisPeri_ExStrSup_1 250 0 4 0
2007 17Networks_RH_SomMotA_1 74 131 182 0
2008 17Networks_RH_SomMotA_2 74 131 183 0
2009 17Networks_RH_SomMotA_3 74 131 184 0
2010 17Networks_RH_SomMotA_4 74 131 185 0
2011 17Networks_RH_SomMotB_Aud_1 47 205 165 0
2012 17Networks_RH_SomMotB_S2_1 47 205 166 0
2013 17Networks_RH_SomMotB_S2_2 47 205 167 0
2014 17Networks_RH_SomMotB_Cent_1 47 205 168 0
2015 17Networks_RH_DorsAttnA_TempOcc_1 79 155 62 0
2016 17Networks_RH_DorsAttnA_ParOcc_1 79 155 63 0
2017 17Networks_RH_DorsAttnA_SPL_1 79 155 64 0
2018 17Networks_RH_DorsAttnB_PostC_1 5 118 16 0
2019 17Networks_RH_DorsAttnB_PostC_2 5 118 17 0
2020 17Networks_RH_DorsAttnB_FEF_1 5 119 15 0
2021 17Networks_RH_SalVentAttnA_ParOper_1 200 58 250 0
2022 17Networks_RH_SalVentAttnA_Ins_1 199 58 251 0
2023 17Networks_RH_SalVentAttnA_ParMed_1 199 57 251 0
2024 17Networks_RH_SalVentAttnA_FrMed_1 199 57 252 0
2025 17Networks_RH_SalVentAttnB_IPL_1 250 152 214 0
2026 17Networks_RH_SalVentAttnB_PFCl_1 250 151 214 0
2027 17Networks_RH_SalVentAttnB_PFCmp_1 250 153 214 0
2028 17Networks_RH_LimbicB_OFC_1 126 135 52 0
2029 17Networks_RH_LimbicA_TempPole_1 224 248 166 0
2030 17Networks_RH_ContA_IPS_1 234 147 35 0
2031 17Networks_RH_ContA_PFCl_1 233 148 35 0
2032 17Networks_RH_ContA_PFCl_2 233 148 36 0
2033 17Networks_RH_ContB_Temp_1 140 51 76 0
2034 17Networks_RH_ContB_IPL_1 139 50 74 0
2035 17Networks_RH_ContB_PFCld_1 139 49 75 0
2036 17Networks_RH_ContB_PFClv_1 139 49 74 0
2037 17Networks_RH_ContC_Cingp_1 123 141 177 0
2038 17Networks_RH_ContC_pCun_1 123 141 178 0
2039 17Networks_RH_DefaultA_IPL_1 251 254 2 0
2040 17Networks_RH_DefaultA_PFCd_1 251 255 3 0
2041 17Networks_RH_DefaultA_pCunPCC_1 251 253 1 0
2042 17Networks_RH_DefaultA_PFCm_1 249 255 1 0
2043 17Networks_RH_DefaultB_PFCd_1 210 63 80 0
2044 17Networks_RH_DefaultB_PFCv_1 209 62 78 0
2045 17Networks_RH_DefaultB_PFCv_2 209 62 79 0
2046 17Networks_RH_DefaultC_Rsp_1 5 0 131 0
2047 17Networks_RH_DefaultC_PHC_1 5 0 132 0
2048 17Networks_RH_TempPar_1 16 48 255 0
2049 17Networks_RH_TempPar_2 13 41 250 0
2050 17Networks_RH_TempPar_3 13 41 251 0
Hi ecla,
THANKS FOR REPLY!
I understood the main idea is to change the original LUTs to an ordered one. And just like what you said ‘the file is out there’. However, this still didn’t work well in my datasets. So I changed my atlas by using Glasser (HCP), and following the tutorial of BATMAN.
this is the my mif image after lableconvert according to the original and ordered LUTs file, I think this because of some kind of nearestneighbor methods?
And this is the SC matrix by using Glasser atlas, I think it’s accurate on some level.
best,
deyu
