Hi Lin,
that is under development. We don't have anything we are ready to distribute at this time. Hopefully within the next year though.
cheers Bruce On Mon, 20 Dec 2010, Lin Nga wrote:
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