I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after

In terminal (ASSUMING shell is bash),

   a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5

   b) export SUBJECTS_DIR=`pwd`

   c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot

Reuben A.