Hi all, Please excuse my naive question; I am new to FreeSurfer. I am trying to segment amygdala subregions and can't quite figure out how to do this. I didn't find anything in the tutorials or the freesurfer archives; if there is any documentation on how to do this, could someone point me in the right direction?
Specifically, I'd like the regions listed below (copied from the FreeSurferColorLUT.txt): #No. Label Name: R G B A 7001 Lateral-nucleus 72 132 181 0 7002 Basolateral-nucleus 243 243 243 0 7003 Basal-nucleus 207 63 79 0 7004 Centromedial-nucleus 121 20 135 0 7005 Central-nucleus 197 60 248 0 7006 Medial-nucleus 2 149 2 0 7007 Cortical-nucleus 221 249 166 0 7008 Accessory-Basal-nucleus 232 146 35 0 7009 Corticoamygdaloid-transitio 20 60 120 0 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 7011 Fusion-amygdala-HP-FAH 122 187 222 0 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 7013 Endopiriform-nucleus 10 49 255 0 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 7015 Paralaminar-nucleus 45 205 165 0 7016 Intercalated-nucleus 117 160 175 0 7017 Prepiriform-cortex 221 217 21 0 7018 Periamygdaloid-cortex 20 60 120 0 7019 Envelope-Amygdala 141 21 100 0 7020 Extranuclear-Amydala 225 140 141 0 I've already ran recon-all and have aseg, aparc+aseg, and aparc.a2009+aseg available as outputs. Do I need aparc.a2005s+seg for the regions listed above? If so, how would I obtain it given the outputs of recon-all? Thanks for the help, Lin
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