The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do this, add the following lines to your startup.m

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab FSH;

Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help!

Best wishes

André

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