Hi all,<br><br>I&#39;m running FreeSurfer v4.0.5 and keep getting the following error:<br><br><br>#######################################<br>#-------------------------------------<br>#@# EM Registration Thu Jul 28 16:09:51 EDT 2011<br>

/home/pnlstaff/freesurfer/subjects/ucsd_20110726/mri<br><br> mri_em_register -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta<br><br>using MR volume brainmask.mgz to mask input volume...<br>

reading 1 input volumes...<br>logging results to talairach.log<br>reading &#39;/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca&#39;...<br>average std = 6.9   using min determinant for regularization = 4.7<br>0 singular and 1812 ill-conditioned covariance matrices regularized<br>

reading &#39;nu.mgz&#39;...<br>freeing gibbs priors...done.<br>bounding unknown intensity as &lt; 14.9 or &gt; 790.2<br>total sample mean = 84.0 (478 zeros)<br>************************************************<br>spacing=8, using 2185 sample points, tol=1.00e-05...<br>

************************************************<br>register_mri: find_optimal_transform<br>find_optimal_transform: nsamples 2185, passno 0, spacing 8<br>GCAhistoScaleImageIntensities: could not find wm peak<br>resetting wm mean[0]: 102 --&gt; 107<br>

resetting gm mean[0]: 64 --&gt; 64<br>input volume #1 is the most T1-like<br>using real data threshold=29.0<br>using (130, 118, 99) as brain centroid...<br>mean wm in atlas = 107, using box (130,93,92) --&gt; (129, 143,105) to find MRI wm<br>

before smoothing, mri peak at 0<br>after smoothing, mri peak at 0, scaling input intensities by inf<br>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<br><br>recon-all exited with ERRORS at Thu Jul 28 16:11:08 EDT 2011<br>

<br>Any ideas?<br><br>Thanks!<br clear="all"><br>-- <br>Talis M. Swisher, BA<br>Research Assistant<br>Psychiatry Neuroimaging Laboratory<br>Harvard Medical School, Brigham and Women&#39;s Hospital<br>1249 Boylston St, 3rd Floor<br>

Boston, MA 02215<br>
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