[MINC-users] Failure of nu-estimate on older t1-weighted brain data.

[Najmeh Khalili M.]

I agree that using an ICBM mask on a native data is not reasonable, but it
worked for most of the cases. However, what is more important is that you
can nu_correct this same data without any mask!

No, I am not using the standard install! Perhaps Yasser can comment on the
quarantine that Dale built for new version of CIVET. I ran PMP on ACES
cluster. More informed comments about machines and the installation
of tools? Perhaps from Andrew, Jason, Yasser, Dale???

N.

On Tue, 28 Feb 2006, Alex ZIJDENBOS wrote:

> I'm not sure what could be going on here; Najma sent me some of the
> data she used and I ran it through nu_correct v1.10 just fine. I'm not
> sure why essentially the same version of n3 would behave differently
> on these data. Are you using a standard install, or a quarantined
> version? The CachedArray error seems to indicate a failure in creating
> a temporary file - that could be a machine resource problem (out of
> /tmp space?).
>
> As for the masking, it seems you are trying to mask a native file with
> a stereotaxic mask, which is likely to produce unexpected results ;) I
> thought N3 checked at least that the sampling lattice of the source
> file and mask are the same - it *should* exit gracefully on something
> like this.
>
> -- A
>
> On Tue, Feb 28, 2006 at 07:18:25PM -0500, Najmeh Khalili M. wrote:
> >
> > Greetings,
> >
> > I am trying to perform N3 on t1-data of healthy older brains and I
> > encounter two error messages. (nu_estimate, version 1.10)
> >
> > First, I got the following error for N=50 data sets:
> >
> >  Assertion failed at line 742 in file templates/CachedArray.cc
> >  nu_estimate_np_and_em: crashed while running volume_stats (termination
> > status=256)
> >
> > Next, I used an ICBM mask; succeeded in non-uniformity correction of N=45
> > data sets, but failed in 5 with :
> >
> >   Direction cosines of mask.mnc and /tmp/native_t1.mnc do not match
> >   Failed to shrink mask volume.
> >   nu_estimate: crashed while running nu_estimate_np_and_em (termination
> >   status=65280)
> >
> > The data dimension in the failed cases is identical to those that have
> > succeeded. The data quality and the brain structure in failing cases is
> > not visually different. I have not seen this problem in younger brains.
> >
> > Has someone else experienced such errors and can any one give an
> > explanation of what the cause of this might be, please?
> >
> > Best,
> > Najma
> >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
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