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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
