Hi Elisabeth,
if you send us a sample dataset we'll take a look. You might also try the newest version as we did fix some bugs in this code.
cheers, Bruce
On Tue, 21 Apr 2009, Wenger, Elisabeth wrote:
Dear freesurfer specialists,
we just ran a sample of subjects, and in a few of them the following problem occured: freesurfer exited with error during em registration, telling us that the wm peak could not be found. The protocol looks like this:
#@# EM Registration Tue Mar 24 18:47:53 CET 2009 /Applications/freesurfer/subjects/hu66B/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=12.9 skull bounding box = (61, 32, 28) --> (196, 145, 201) using (106, 70, 115) as brain centroid... mean wm in atlas = 107, using box (89,56,94) --> (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 mpib4003.mpib-berlin.mpg.de 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 Tue Mar 24 18:48:48 CET 2009
We are 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. Thank you for your help!
Best, Elisabeth and Shireen