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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 7.4.1516 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
directoryerror: mri_cc: no WM voxels found with norm > 40 -- check skull
strippingBests,J.
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