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