Hi ! First time poster here (and aware that this could be a very amateur question)
I have run qsiprep and qsirecon on some data - and just wanted to double check whether the following was an issue.
As far as I know, for the LUT created using labelconvert (e.g. for a Schaefer100x parcellation), the numbers must increment by 1 - but I have noticed that across the board for the different atlases created by qsiprep, a region in the subcortex is missing in each LUT: see below example from Schae 100x (region 101 is missing).
90 RH_Default_Par_1
91 RH_Default_Temp_1
92 RH_Default_Temp_2
93 RH_Default_Temp_3
94 RH_Default_PFCv_1
95 RH_Default_PFCv_2
96 RH_Default_PFCm_1
97 RH_Default_PFCm_2
98 RH_Default_PFCm_3
99 RH_Default_PCC_1
100 RH_Default_PCC_2
102 CIT168Subcortical_Pu_rh
103 CIT168Subcortical_Ca_rh
104 CIT168Subcortical_NAC_rh
105 CIT168Subcortical_EXA_rh
106 CIT168Subcortical_GPe_rh
107 CIT168Subcortical_GPi_rh
108 CIT168Subcortical_SNc_CIT168Subcortical_PBP_CIT168Subcortical_VTA_rh
109 CIT168Subcortical_RN_rh
110 CIT168Subcortical_SNr_rh
111 CIT168Subcortical_VeP_rh
112 CIT168Subcortical_HN_rh
113 CIT168Subcortical_HTH_rh
114 CIT168Subcortical_MN_rh
115 CIT168Subcortical_STH_rh
116 CIT168Subcortical_Pu_lh
117 CIT168Subcortical_Ca_lh
118 CIT168Subcortical_NAC_lh
119 CIT168Subcortical_EXA_lh
120 CIT168Subcortical_GPe_lh
121 CIT168Subcortical_GPi_lh
122 CIT168Subcortical_SNc_CIT168Subcortical_PBP_CIT168Subcortical_VTA_lh
123 CIT168Subcortical_RN_lh
124 CIT168Subcortical_SNr_lh
125 CIT168Subcortical_VeP_lh
126 CIT168Subcortical_HN_lh
127 CIT168Subcortical_HTH_lh
128 CIT168Subcortical_MN_lh
129 CIT168Subcortical_STH_lh
QSIPrep and QSIRecon execute without any issues flagged - but I am concerned that this could be an error (and that an error flag should be raised).
Any help here would be greatly appreciated 
Best
T