Hi Tali
did you check the skull stripping to make sure it didn't fail?
Bruce
On Fri, 29 Jul 2011, Tali Swisher wrote:
Hi all,
I'm running FreeSurfer v4.0.5 and keep getting the following error:
####################################### #------------------------------------- #@# EM Registration Thu Jul 28 16:09:51 EDT 2011 /home/pnlstaff/freesurfer/subjects/ucsd_20110726/mri
mri_em_register -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/share/apps/freesurfer4.0.5/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=29.0 using (130, 118, 99) as brain centroid... mean wm in atlas = 107, using box (130,93,92) --> (129, 143,105) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux compute-4-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Jul 28 16:11:08 EDT 2011
Any ideas?
Thanks!
-- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150