Dear Paul, 1) You find pretty thoroughful info on expert options file here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences
2) recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp and -autorecon2-wm runs the same commands, at least in version 6.0). 3) There is in the souce code following comment on -T option in mri_fill: min # of neighbors which must be on to retain a point Default value is 1. Regards, Antonin Hello Freesurfer, I have couple questions. 1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30) and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag with recon? 2) If I have added control points and wm edits to a subject, it is accurate to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 3) Lastly, I am playing around with mri_fill command and I did like to know what -T flag does? Thank you Best, Paul
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