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
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