Hi Elisabeth,
try running recon-all with -no-wsgcaatlas and see if that fixes your
problem.
cheers,
Bruce
On Mon, 19 Apr 2010, Wenger, Elisabeth wrote:
Dear freesurfer specialists,
we just ran a sample of 91 subjects (with 3 timepoints), and in 5 of them the
following problem occured: freesurfer exited with error in autorecon1 during
skull stripping. The protocol looks like this:
#--------------------------------------------
#...@# Skull Stripping Thu Sep 17 18:13:23 CEST 2009
/Applications/freesurfer/subjects/1115is05B/mri
\n mri_em_register -skull nu.mgz
/Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta \n
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1 using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
GCAhistoScaleImageIntensities: could not find wm peak
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=9.0
skull bounding box = (51, 10, 25) --> (205, 255, 237)
using (102, 92, 131) as brain centroid...
mean wm in atlas = 126, using box (83,62,105) --> (120, 122,157) to find MRI wm
before smoothing, mri peak at 0
after smoothing, mri peak at 0, scaling input intensities by inf
Darwin LIP-bxp-164-3.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24
17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386
recon-all exited with ERRORS at Thu Sep 17 18:14:19 CEST 2009
We are pretty much freesurfer beginners and don't have a clue what kind of
mistake this could be. We couldn't find any obvious differnces to our other
subjects which ran fine. I also attach the whole recon-all.log file, just in
case a problem occured on a previous stage we didn't recognize. We used a
MacPro3,1 and Freesurfer version 4.2.0.
Thank you for your help!
Best,
Elisabeth and Genia
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