did you look at the results (eg, the aseg)? Can you send the recon-all.log file?
On 11/19/2023 11:18 PM, June Kang wrote:
External Email - Use Caution
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,
J.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer