Dear Freesurfer specialists,
to fix the skull stripping error, i tried running "recon-all with -no-wsgcaatlas", as you suggested. This seems to have fixed the skull stripping thing, but now there is again an error in the EM registration step - just as in a few other subjects of our sample... The script looks like this:
#@# EM Registration Thu Apr 22 11:24:12 CEST 2010 /Applications/freesurfer/subjects/1115is05B/mri \n mri_em_register -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta \n using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (61, 33, 24) --> (195, 145, 204) using (106, 70, 114) as brain centroid... mean wm in atlas = 107, using box (90,56,92) --> (122, 83,136) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin LIP-OSX-164-15.local 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc
recon-all exited with ERRORS at Thu Apr 22 11:26:00 CEST 2010
Again, i attach the full recon-log file. Thanks a lot a lot a lot for your help!!
Best, Elisabeth