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

[Kelvin Mok]

Hi Najma,

Using the same quarantine, I received errors running nu_estimate in the 
past as well. The errors were different and potentially caused by memory 
leak (or lack of memory?) within function nu_estimate_np_and_em - but I 
never encountered them again. Not sure if this helps.

Kelvin


Najmeh Khalili M. wrote:

> 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
>>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>_______________________________________________
>>MINC-users at bic.mni.mcgill.ca
>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> 
> 
> 
> 
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