Discrepancy in parcellation images from a given FreeSurfer output

Dear MRtrixters,
I am working with HCP data, and have generated two parcellation images along with a 5TT (hsvs) image. All three images have been generated using the same FreeSurfer outputs. The parcellation images include:

I have noticed that the cortical ribbon in the DK parcellation image matches up with the cortical ribbon in the 5TT image (attached, left figure). However, the cortical ribbon in the HCPMMP1 image has a few (possibly problematic) differences compared to the 5TT image (right figure, see crosshair).

Any ideas on why the ribbon thickness is different between the two parcellation images, and, how to generate a HCPMMP1 parcellation image with the same ribbon thickness as the 5TT image?

Cheers,
Arkiev

Hi Arkiev,

I’m not sure why this would happen although it looks like a local rather than a global problem - seems like the label is completely missing there so perhaps worth debugging the steps in the creation of the parcellation.

In the past, I’ve used the script from here to obtain satisfactory HCPMMP1 parcellations after running recon-all.

All the best,
Nick

Hi Nick,
Thanks for getting back to me so soon - your recommendation worked well :slight_smile:

The next step is to re-index the parcellation file to have nodes incrementing from 1. I am unsure how to address this with the available outputs - in particular, LUT_HCPMMP1.txt. This lookup table doesn’t seem to match up with the values in HCPMMP1.nii.gz (for example, node 28 is present in HCPMMP1.nii.gz but is absent from LUT_HCPMMP1.txt).

I have pasted the contents of LUT_HCPMMP1.txt below - is this a sensible output, or has something gone wrong?

Also, do you know where I can access the lut_in and lut_out files for labelconvert?

Again, thanks for your help!

1001	lh.???.label
1002	lh.L_V1_ROI.label
1003	lh.L_MST_ROI.label
1004	lh.L_V6_ROI.label
1005	lh.L_V2_ROI.label
1006	lh.L_V3_ROI.label
1007	lh.L_V4_ROI.label
1008	lh.L_V8_ROI.label
1009	lh.L_4_ROI.label
1010	lh.L_3b_ROI.label
1011	lh.L_FEF_ROI.label
1012	lh.L_PEF_ROI.label
1013	lh.L_55b_ROI.label
1014	lh.L_V3A_ROI.label
1015	lh.L_RSC_ROI.label
1016	lh.L_POS2_ROI.label
1017	lh.L_V7_ROI.label
1018	lh.L_IPS1_ROI.label
1019	lh.L_FFC_ROI.label
1020	lh.L_V3B_ROI.label
1021	lh.L_LO1_ROI.label
1022	lh.L_LO2_ROI.label
1023	lh.L_PIT_ROI.label
1024	lh.L_MT_ROI.label
1025	lh.L_A1_ROI.label
1026	lh.L_PSL_ROI.label
1027	lh.L_SFL_ROI.label
1028	lh.L_PCV_ROI.label
1029	lh.L_STV_ROI.label
1030	lh.L_7Pm_ROI.label
1031	lh.L_7m_ROI.label
1032	lh.L_POS1_ROI.label
1033	lh.L_23d_ROI.label
1034	lh.L_v23ab_ROI.label
1035	lh.L_d23ab_ROI.label
1036	lh.L_31pv_ROI.label
1037	lh.L_5m_ROI.label
1038	lh.L_5mv_ROI.label
1039	lh.L_23c_ROI.label
1040	lh.L_5L_ROI.label
1041	lh.L_24dd_ROI.label
1042	lh.L_24dv_ROI.label
1043	lh.L_7AL_ROI.label
1044	lh.L_SCEF_ROI.label
1045	lh.L_6ma_ROI.label
1046	lh.L_7Am_ROI.label
1047	lh.L_7PL_ROI.label
1048	lh.L_7PC_ROI.label
1049	lh.L_LIPv_ROI.label
1050	lh.L_VIP_ROI.label
1051	lh.L_MIP_ROI.label
1052	lh.L_1_ROI.label
1053	lh.L_2_ROI.label
1054	lh.L_3a_ROI.label
1055	lh.L_6d_ROI.label
1056	lh.L_6mp_ROI.label
1057	lh.L_6v_ROI.label
1058	lh.L_p24pr_ROI.label
1059	lh.L_33pr_ROI.label
1060	lh.L_a24pr_ROI.label
1061	lh.L_p32pr_ROI.label
1062	lh.L_a24_ROI.label
1063	lh.L_d32_ROI.label
1064	lh.L_8BM_ROI.label
1065	lh.L_p32_ROI.label
1066	lh.L_10r_ROI.label
1067	lh.L_47m_ROI.label
1068	lh.L_8Av_ROI.label
1069	lh.L_8Ad_ROI.label
1070	lh.L_9m_ROI.label
1071	lh.L_8BL_ROI.label
1072	lh.L_9p_ROI.label
1073	lh.L_10d_ROI.label
1074	lh.L_8C_ROI.label
1075	lh.L_44_ROI.label
1076	lh.L_45_ROI.label
1077	lh.L_47l_ROI.label
1078	lh.L_a47r_ROI.label
1079	lh.L_6r_ROI.label
1080	lh.L_IFJa_ROI.label
1081	lh.L_IFJp_ROI.label
1082	lh.L_IFSp_ROI.label
1083	lh.L_IFSa_ROI.label
1084	lh.L_p9-46v_ROI.label
1085	lh.L_46_ROI.label
1086	lh.L_a9-46v_ROI.label
1087	lh.L_9-46d_ROI.label
1088	lh.L_9a_ROI.label
1089	lh.L_10v_ROI.label
1090	lh.L_a10p_ROI.label
1091	lh.L_10pp_ROI.label
1092	lh.L_11l_ROI.label
1093	lh.L_13l_ROI.label
1094	lh.L_OFC_ROI.label
1095	lh.L_47s_ROI.label
1096	lh.L_LIPd_ROI.label
1097	lh.L_6a_ROI.label
1098	lh.L_i6-8_ROI.label
1099	lh.L_s6-8_ROI.label
1100	lh.L_43_ROI.label
1101	lh.L_OP4_ROI.label
1102	lh.L_OP1_ROI.label
1103	lh.L_OP2-3_ROI.label
1104	lh.L_52_ROI.label
1105	lh.L_RI_ROI.label
1106	lh.L_PFcm_ROI.label
1107	lh.L_PoI2_ROI.label
1108	lh.L_TA2_ROI.label
1109	lh.L_FOP4_ROI.label
1110	lh.L_MI_ROI.label
1111	lh.L_Pir_ROI.label
1112	lh.L_AVI_ROI.label
1113	lh.L_AAIC_ROI.label
1114	lh.L_FOP1_ROI.label
1115	lh.L_FOP3_ROI.label
1116	lh.L_FOP2_ROI.label
1117	lh.L_PFt_ROI.label
1118	lh.L_AIP_ROI.label
1119	lh.L_EC_ROI.label
1120	lh.L_PreS_ROI.label
1122	lh.L_ProS_ROI.label
1123	lh.L_PeEc_ROI.label
1124	lh.L_STGa_ROI.label
1125	lh.L_PBelt_ROI.label
1126	lh.L_A5_ROI.label
1127	lh.L_PHA1_ROI.label
1128	lh.L_PHA3_ROI.label
1129	lh.L_STSda_ROI.label
1130	lh.L_STSdp_ROI.label
1131	lh.L_STSvp_ROI.label
1132	lh.L_TGd_ROI.label
1133	lh.L_TE1a_ROI.label
1134	lh.L_TE1p_ROI.label
1135	lh.L_TE2a_ROI.label
1136	lh.L_TF_ROI.label
1137	lh.L_TE2p_ROI.label
1138	lh.L_PHT_ROI.label
1139	lh.L_PH_ROI.label
1140	lh.L_TPOJ1_ROI.label
1141	lh.L_TPOJ2_ROI.label
1142	lh.L_TPOJ3_ROI.label
1143	lh.L_DVT_ROI.label
1144	lh.L_PGp_ROI.label
1145	lh.L_IP2_ROI.label
1146	lh.L_IP1_ROI.label
1147	lh.L_IP0_ROI.label
1148	lh.L_PFop_ROI.label
1149	lh.L_PF_ROI.label
1150	lh.L_PFm_ROI.label
1151	lh.L_PGi_ROI.label
1152	lh.L_PGs_ROI.label
1153	lh.L_V6A_ROI.label
1154	lh.L_VMV1_ROI.label
1155	lh.L_VMV3_ROI.label
1156	lh.L_PHA2_ROI.label
1157	lh.L_V4t_ROI.label
1158	lh.L_FST_ROI.label
1159	lh.L_V3CD_ROI.label
1160	lh.L_LO3_ROI.label
1161	lh.L_VMV2_ROI.label
1162	lh.L_31pd_ROI.label
1163	lh.L_31a_ROI.label
1164	lh.L_VVC_ROI.label
1165	lh.L_25_ROI.label
1166	lh.L_s32_ROI.label
1167	lh.L_pOFC_ROI.label
1168	lh.L_PoI1_ROI.label
1169	lh.L_Ig_ROI.label
1170	lh.L_FOP5_ROI.label
1171	lh.L_p10p_ROI.label
1172	lh.L_p47r_ROI.label
1173	lh.L_TGv_ROI.label
1174	lh.L_MBelt_ROI.label
1175	lh.L_LBelt_ROI.label
1176	lh.L_A4_ROI.label
1177	lh.L_STSva_ROI.label
1178	lh.L_TE1m_ROI.label
1179	lh.L_PI_ROI.label
1180	lh.L_a32pr_ROI.label
1181	lh.L_p24_ROI.label
2001	rh.???.label
2002	rh.R_V1_ROI.label
2003	rh.R_MST_ROI.label
2004	rh.R_V6_ROI.label
2005	rh.R_V2_ROI.label
2006	rh.R_V3_ROI.label
2007	rh.R_V4_ROI.label
2008	rh.R_V8_ROI.label
2009	rh.R_4_ROI.label
2010	rh.R_3b_ROI.label
2011	rh.R_FEF_ROI.label
2012	rh.R_PEF_ROI.label
2013	rh.R_55b_ROI.label
2014	rh.R_V3A_ROI.label
2015	rh.R_RSC_ROI.label
2016	rh.R_POS2_ROI.label
2017	rh.R_V7_ROI.label
2018	rh.R_IPS1_ROI.label
2019	rh.R_FFC_ROI.label
2020	rh.R_V3B_ROI.label
2021	rh.R_LO1_ROI.label
2022	rh.R_LO2_ROI.label
2023	rh.R_PIT_ROI.label
2024	rh.R_MT_ROI.label
2025	rh.R_A1_ROI.label
2026	rh.R_PSL_ROI.label
2027	rh.R_SFL_ROI.label
2028	rh.R_PCV_ROI.label
2029	rh.R_STV_ROI.label
2030	rh.R_7Pm_ROI.label
2031	rh.R_7m_ROI.label
2032	rh.R_POS1_ROI.label
2033	rh.R_23d_ROI.label
2034	rh.R_v23ab_ROI.label
2035	rh.R_d23ab_ROI.label
2036	rh.R_31pv_ROI.label
2037	rh.R_5m_ROI.label
2038	rh.R_5mv_ROI.label
2039	rh.R_23c_ROI.label
2040	rh.R_5L_ROI.label
2041	rh.R_24dd_ROI.label
2042	rh.R_24dv_ROI.label
2043	rh.R_7AL_ROI.label
2044	rh.R_SCEF_ROI.label
2045	rh.R_6ma_ROI.label
2046	rh.R_7Am_ROI.label
2047	rh.R_7PL_ROI.label
2048	rh.R_7PC_ROI.label
2049	rh.R_LIPv_ROI.label
2050	rh.R_VIP_ROI.label
2051	rh.R_MIP_ROI.label
2052	rh.R_1_ROI.label
2053	rh.R_2_ROI.label
2054	rh.R_3a_ROI.label
2055	rh.R_6d_ROI.label
2056	rh.R_6mp_ROI.label
2057	rh.R_6v_ROI.label
2058	rh.R_p24pr_ROI.label
2059	rh.R_33pr_ROI.label
2060	rh.R_a24pr_ROI.label
2061	rh.R_p32pr_ROI.label
2062	rh.R_a24_ROI.label
2063	rh.R_d32_ROI.label
2064	rh.R_8BM_ROI.label
2065	rh.R_p32_ROI.label
2066	rh.R_10r_ROI.label
2067	rh.R_47m_ROI.label
2068	rh.R_8Av_ROI.label
2069	rh.R_8Ad_ROI.label
2070	rh.R_9m_ROI.label
2071	rh.R_8BL_ROI.label
2072	rh.R_9p_ROI.label
2073	rh.R_10d_ROI.label
2074	rh.R_8C_ROI.label
2075	rh.R_44_ROI.label
2076	rh.R_45_ROI.label
2077	rh.R_47l_ROI.label
2078	rh.R_a47r_ROI.label
2079	rh.R_6r_ROI.label
2080	rh.R_IFJa_ROI.label
2081	rh.R_IFJp_ROI.label
2082	rh.R_IFSp_ROI.label
2083	rh.R_IFSa_ROI.label
2084	rh.R_p9-46v_ROI.label
2085	rh.R_46_ROI.label
2086	rh.R_a9-46v_ROI.label
2087	rh.R_9-46d_ROI.label
2088	rh.R_9a_ROI.label
2089	rh.R_10v_ROI.label
2090	rh.R_a10p_ROI.label
2091	rh.R_10pp_ROI.label
2092	rh.R_11l_ROI.label
2093	rh.R_13l_ROI.label
2094	rh.R_OFC_ROI.label
2095	rh.R_47s_ROI.label
2096	rh.R_LIPd_ROI.label
2097	rh.R_6a_ROI.label
2098	rh.R_i6-8_ROI.label
2099	rh.R_s6-8_ROI.label
2100	rh.R_43_ROI.label
2101	rh.R_OP4_ROI.label
2102	rh.R_OP1_ROI.label
2103	rh.R_OP2-3_ROI.label
2104	rh.R_52_ROI.label
2105	rh.R_RI_ROI.label
2106	rh.R_PFcm_ROI.label
2107	rh.R_PoI2_ROI.label
2108	rh.R_TA2_ROI.label
2109	rh.R_FOP4_ROI.label
2110	rh.R_MI_ROI.label
2111	rh.R_Pir_ROI.label
2112	rh.R_AVI_ROI.label
2113	rh.R_AAIC_ROI.label
2114	rh.R_FOP1_ROI.label
2115	rh.R_FOP3_ROI.label
2116	rh.R_FOP2_ROI.label
2117	rh.R_PFt_ROI.label
2118	rh.R_AIP_ROI.label
2119	rh.R_EC_ROI.label
2120	rh.R_PreS_ROI.label
2122	rh.R_ProS_ROI.label
2123	rh.R_PeEc_ROI.label
2124	rh.R_STGa_ROI.label
2125	rh.R_PBelt_ROI.label
2126	rh.R_A5_ROI.label
2127	rh.R_PHA1_ROI.label
2128	rh.R_PHA3_ROI.label
2129	rh.R_STSda_ROI.label
2130	rh.R_STSdp_ROI.label
2131	rh.R_STSvp_ROI.label
2132	rh.R_TGd_ROI.label
2133	rh.R_TE1a_ROI.label
2134	rh.R_TE1p_ROI.label
2135	rh.R_TE2a_ROI.label
2136	rh.R_TF_ROI.label
2137	rh.R_TE2p_ROI.label
2138	rh.R_PHT_ROI.label
2139	rh.R_PH_ROI.label
2140	rh.R_TPOJ1_ROI.label
2141	rh.R_TPOJ2_ROI.label
2142	rh.R_TPOJ3_ROI.label
2143	rh.R_DVT_ROI.label
2144	rh.R_PGp_ROI.label
2145	rh.R_IP2_ROI.label
2146	rh.R_IP1_ROI.label
2147	rh.R_IP0_ROI.label
2148	rh.R_PFop_ROI.label
2149	rh.R_PF_ROI.label
2150	rh.R_PFm_ROI.label
2151	rh.R_PGi_ROI.label
2152	rh.R_PGs_ROI.label
2153	rh.R_V6A_ROI.label
2154	rh.R_VMV1_ROI.label
2155	rh.R_VMV3_ROI.label
2156	rh.R_PHA2_ROI.label
2157	rh.R_V4t_ROI.label
2158	rh.R_FST_ROI.label
2159	rh.R_V3CD_ROI.label
2160	rh.R_LO3_ROI.label
2161	rh.R_VMV2_ROI.label
2162	rh.R_31pd_ROI.label
2163	rh.R_31a_ROI.label
2164	rh.R_VVC_ROI.label
2165	rh.R_25_ROI.label
2166	rh.R_s32_ROI.label
2167	rh.R_pOFC_ROI.label
2168	rh.R_PoI1_ROI.label
2169	rh.R_Ig_ROI.label
2170	rh.R_FOP5_ROI.label
2171	rh.R_p10p_ROI.label
2172	rh.R_p47r_ROI.label
2173	rh.R_TGv_ROI.label
2174	rh.R_MBelt_ROI.label
2175	rh.R_LBelt_ROI.label
2176	rh.R_A4_ROI.label
2177	rh.R_STSva_ROI.label
2178	rh.R_TE1m_ROI.label
2179	rh.R_PI_ROI.label
2180	rh.R_a32pr_ROI.label
2181	rh.R_p24_ROI.label

Cheers,
Arkiev

Hey,

Glad to hear that it worked!

It can happen that a participant misses a certain parcel - depending on their anatomy - so don’t use the participant LUTs from the output of that script, as they will only contain the labels present in that participant.

You can find the files for labelconvert here. hcpmmp1_original is the reference LUT and hcpmmp1_ordered gives the desired order for the output.

Good luck,
Nick

1 Like

Hi Nick,
Thanks for your help - problem solved :smiley:

Cheers,
Arkiev

1 Like