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