Hi!
recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
looks good. The flag -hippocampal-subfields-T1FLAIR does not even exist ;-)
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 3 Feb 2017, at 11:32, Erik O'Hanlon <erikohanlon@rcsi.ie> wrote:

recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair