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It usual to have many FreeSurfer recon-all commands to process multiple datasets.

This procedure helps to automate this: 

cd your_study_group_data
SETENV SUBJECTS_DIR $PWD
foreach i (*)
echo $i
recon-all -subjid $i -all
end

Wait some days...

UserContributions/Scripts/Two (last edited 2016-10-18 16:48:21 by 172)