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Hello,

According to the FAQ for earlier version of Freesurfer (maybe 6.x), the instruction is below.

First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s <subjid>

Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s <subjid>

The autorecon1 step works good, however, second step ends with error repeatedly in 7.4.1

516 voxels in left wm, 1068 in right wm, xrange [124, 129]

searching rotation angles z=[-7 7], y=[83 97]

searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)

final transformation (x=0.0, yr=90.000, zr=-0.000):

-0.00000 0.00000 1.00000 128.00000;

0.00000 1.00000 0.00000 128.00000;

-1.00000 0.00000 -0.00000 127.99999;

0.00000 0.00000 0.00000 1.00000;

error: No such file or directory

error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping

Bests,