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
#-------------------------------------------- #@# 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 #-------------------------------------------- #@# 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 #-------------------------------------------- #@# 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