Jerry, At this point, I think Bruce will need to jump-in to answer (he is out- of-town today). I think he will ask about your scan parameters, ie, how is your scanner setup? It sounds as if something is not quite right in the data coming-off the scanner.
Nick On Tue, 2008-04-22 at 14:26 -0400, Jerry Yeou-Wei Chen wrote: > Thanks for the reply, Nick. I think you correctly identified the > problem. > nu.mgz is oriented correctly, but looks very dark... However, it looks > decent if I adjust the brightness/contrast.... > I have other scans that were processed without error, and the > orig.mgz, and nu.mgz also appear quite dark (and the mri peaks are > very low, too: 29, 46, 52, ...) Also, for those successfully > processed, the brainmask.mgz looks decent as well. > Perhaps this scan that exited with error was too dark to be corrected > by the intensity normalization algorithm? > > - Jerry > > On Tue, Apr 22, 2008 at 1:22 PM, Nick Schmansky > <[EMAIL PROTECTED]> wrote: > 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 > > _______________________________________________ > 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
