Jerry, I'm not sure why it exited without giving a better message, but this is a clue why it exited:
before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf the mri peak is at zero, which is wrong (it should be around 116/117 or so). if you view nu.mgz (tkmedit -f nu.mgz), does it look ok? is it oriented correctly? Nick On Tue, 2008-04-22 at 12:28 -0400, Jerry Yeou-Wei Chen wrote: > Hello, > > I am having trouble deciphering why I got the error attached below. > Any suggestions would be greatly appreciated! > > Thanks, > - Jerry > > > > > Tue Apr 22 10:15:22 EDT 2008 > talairach_avi done > > cp transforms/talairach.auto.xfm transforms/talairach.xfm > > #-------------------------------------------- > [EMAIL PROTECTED] Talairach Failure Detection Tue Apr 22 10:15:23 EDT 2008 > /scratch/freesurfer/subjects/17/s017/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > talairach_afd: Talairach Transform: transforms/talairach.xfm OK > (p=0.7072, pval=0.4932 >= threshold=0.0050) > > awk - > f /scratch/freesurfer/bin/extract_talairach_avi_QA.awk > /scratch/freesurfer/subjects/17/s017/mri/transforms/talairach_avi.log > > TalAviQA: 0.96840 > z-score: -2 > #-------------------------------------------- > [EMAIL PROTECTED] Intensity Normalization Tue Apr 22 10:15:23 EDT 2008 > /scratch/freesurfer/subjects/17/s017/mri > > mri_normalize -g 1 nu.mgz T1.mgz > > using max gradient = 1.000 > reading from nu.mgz... > normalizing image... > talairach transform > 0.976 0.083 0.030 -136.866; > -0.072 1.053 0.164 -153.262; > -0.020 -0.109 1.085 -122.101; > 0.000 0.000 0.000 1.000; > INFO: Modifying talairach volume c_(r,a,s) based on average_305 > building Voronoi diagram... > performing soap bubble smoothing... > 3d normalization pass 1 of 2 > building Voronoi diagram... > performing soap bubble smoothing... > 3d normalization pass 2 of 2 > building Voronoi diagram... > performing soap bubble smoothing... > writing output to T1.mgz > 3D bias adjustment took 19 minutes and 44 seconds. > white matter peak found at 111 > gm peak at 88 (88), valley at 80 (80) > csf peak at 57, setting threshold to 77 > white matter peak found at 111 > gm peak at 88 (88), valley at 80 (80) > csf peak at 55, setting threshold to 77 > #-------------------------------------------- > [EMAIL PROTECTED] Skull Stripping Tue Apr 22 10:35:16 EDT 2008 > /scratch/freesurfer/subjects/17/s017/mri > > mri_em_register -skull > nu.mgz /scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca > transforms/talairach_with_skull.lta > > aligning to atlas containing skull, setting unknown_nbr_spacing = 5 > reading 1 input volumes... > logging results to talairach_with_skull.log > reading > '/scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca'... > average std = 23.1 using min determinant for regularization = 53.4 > 0 singular and 5702 ill-conditioned covariance matrices regularized > reading 'nu.mgz'... > freeing gibbs priors...done. > bounding unknown intensity as < 20.2 or > 943.7 > total sample mean = 92.0 (1443 zeros) > ************************************************ > spacing=8, using 3481 sample points, tol=1.00e-05... > ************************************************ > register_mri: find_optimal_transform > find_optimal_transform: nsamples 3481, passno 0, spacing 8 > GCAhistoScaleImageIntensities: could not find wm peak > resetting wm mean[0]: 117 --> 126 > resetting gm mean[0]: 74 --> 74 > input volume #1 is the most T1-like > using real data threshold=9.0 > using (102, 110, 122) as brain centroid... > mean wm in atlas = 126, using box (80,83,98) --> (123, 136,146) to > find MRI wm > before smoothing, mri peak at 0 > after smoothing, mri peak at 0, scaling input intensities by inf > Linux kdavis8-efef.uhnres.utoronto.ca 2.6.23.1-21.fc7 #1 SMP Thu Nov 1 > 21:09:24 EDT 2007 i686 i686 i386 GNU/Linux > > recon-all exited with ERRORS at Tue Apr 22 10:41:40 EDT 2008 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
