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To whom it may concern,
I am trying to run hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmy...) on FreeSurfer v6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). I was able to run recon-all, however I am unable to run segmentHA_T1.sh because the command doesn't exist in $FREESURFER_HOME/bin. Instead, there is segmentSF_T1.sh. I've tried searching the email listings for information comparing the two scripts, but haven't been able to find much.
In order to run the hippocampal and amygdala segmentation, am I able to use segmentSF_T1.sh instead of segmentHA_T1.sh? Is there a more recent version of Freesurfer I have to install that includes segmentHA_T1.sh?
Thank you in advance for the help.
Best, CC
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