Hello,<br><br>I am having trouble deciphering why I got the error attached below. Any suggestions would be greatly appreciated!<br><br>Thanks,<br>- Jerry<br><br><br><br><br>Tue Apr 22 10:15:22 EDT 2008<br>talairach_avi done<br>
<br>&nbsp;cp transforms/talairach.auto.xfm transforms/talairach.xfm <br><br>#--------------------------------------------<br>#@# Talairach Failure Detection Tue Apr 22 10:15:23 EDT 2008<br>/scratch/freesurfer/subjects/17/s017/mri<br>
<br>&nbsp;talairach_afd -T 0.005 -xfm transforms/talairach.xfm <br><br>talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7072, pval=0.4932 &gt;= threshold=0.0050)<br><br>&nbsp;awk -f /scratch/freesurfer/bin/extract_talairach_avi_QA.awk /scratch/freesurfer/subjects/17/s017/mri/transforms/talairach_avi.log <br>
<br>TalAviQA: 0.96840<br>z-score: -2<br>#--------------------------------------------<br>#@# Intensity Normalization Tue Apr 22 10:15:23 EDT 2008<br>/scratch/freesurfer/subjects/17/s017/mri<br><br>&nbsp;mri_normalize -g 1 nu.mgz T1.mgz <br>
<br>using max gradient = 1.000<br>reading from nu.mgz...<br>normalizing image...<br>talairach transform<br>&nbsp;0.976&nbsp;&nbsp; 0.083&nbsp;&nbsp; 0.030&nbsp; -136.866;<br>-0.072&nbsp;&nbsp; 1.053&nbsp;&nbsp; 0.164&nbsp; -153.262;<br>-0.020&nbsp; -0.109&nbsp;&nbsp; 1.085&nbsp; -122.101;<br>&nbsp;0.000&nbsp;&nbsp; 0.000&nbsp;&nbsp; 0.000&nbsp;&nbsp; 1.000;<br>
INFO: Modifying talairach volume c_(r,a,s) based on average_305<br>building Voronoi diagram...<br>performing soap bubble smoothing...<br>3d normalization pass 1 of 2<br>building Voronoi diagram...<br>performing soap bubble smoothing...<br>
3d normalization pass 2 of 2<br>building Voronoi diagram...<br>performing soap bubble smoothing...<br>writing output to T1.mgz<br>3D bias adjustment took 19 minutes and 44 seconds.<br>white matter peak found at 111<br>gm peak at 88 (88), valley at 80 (80)<br>
csf peak at 57, setting threshold to 77<br>white matter peak found at 111<br>gm peak at 88 (88), valley at 80 (80)<br>csf peak at 55, setting threshold to 77<br>#--------------------------------------------<br>#@# Skull Stripping Tue Apr 22 10:35:16 EDT 2008<br>
/scratch/freesurfer/subjects/17/s017/mri<br><br>&nbsp;mri_em_register -skull nu.mgz /scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta <br><br>aligning to atlas containing skull, setting unknown_nbr_spacing = 5<br>
reading 1 input volumes...<br>logging results to talairach_with_skull.log<br>reading &#39;/scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca&#39;...<br>average std = 23.1&nbsp;&nbsp; using min determinant for regularization = 53.4<br>
0 singular and 5702 ill-conditioned covariance matrices regularized<br>reading &#39;nu.mgz&#39;...<br>freeing gibbs priors...done.<br>bounding unknown intensity as &lt; 20.2 or &gt; 943.7 <br>total sample mean = 92.0 (1443 zeros)<br>
************************************************<br>spacing=8, using 3481 sample points, tol=1.00e-05...<br>************************************************<br>register_mri: find_optimal_transform<br>find_optimal_transform: nsamples 3481, passno 0, spacing 8<br>
GCAhistoScaleImageIntensities: could not find wm peak<br>resetting wm mean[0]: 117 --&gt; 126<br>resetting gm mean[0]: 74 --&gt; 74<br>input volume #1 is the most T1-like<br>using real data threshold=9.0<br>using (102, 110, 122) as brain centroid...<br>
mean wm in atlas = 126, using box (80,83,98) --&gt; (123, 136,146) 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 <a href="http://kdavis8-efef.uhnres.utoronto.ca">kdavis8-efef.uhnres.utoronto.ca</a> 2.6.23.1-21.fc7 #1 SMP Thu Nov 1 21:09:24 EDT 2007 i686 i686 i386 GNU/Linux<br>
<br>recon-all exited with ERRORS at Tue Apr 22 10:41:40 EDT 2008<br>