p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes nu_correct can create very dark images, and there are some switches you can loo through to correct them. Alternatively if it is the 001.mgz, mri_convert has a scale option you can use.
cheers, Bruce
On Fri, 25 Apr 2008, Jerry Yeou-Wei Chen wrote:
Okay, thanks for your help again Nick! Regarding the scan data: I am actually working with data collected by a previous member of our lab, and there were indeed some problems... (related to the SCIC algorithm on our GE scanner). So, our technician created a program to "uncorrect" the intensity scaling. The images he saved appear dark when we load them freesurfer, but we expected autorecon's intensity normalization would handle this. In fact, autorecon did successfully process 34 out of 35 scans. (the cortical surface appears quite decent for them, and the thickness values on our average subject appears to be within normal range...) I wonder if I should be concerned about our results due to this intensity issue...
On Tue, Apr 22, 2008 at 2:42 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
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 nicks@nmr.mgh.harvard.edu 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 > > #-------------------------------------------- > #@# 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 > _______________________________________________ > 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
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