Hi FS experts,

I have run an analysis using v6.0 and included the hippocampal subfields in the command using combined T1 and Flair segmentation. I would now like to look at the Amygdala segementation as described on the FS wiki. I would like to once again use both by T1 and FLAIR images but am a little confused about how to do that. Does the new tool haev to be run for T1 images and then followed by a second T2 specific run?

for example would the following generate the hippocampus and  amygdala meassures and generate a txt file for each hierarchy (ie HBT.txt, FS60.txt and CA.txt for hippoSF and amygNuc) ? 

segmentHA_T2.sh  subject001  subject001_Flair.nni.gz   T1andFlair  USE_T1  /subject001

   Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir?

Thanks for any help you can provide .

Erik