[Neurodebian-users] Segmentation fault with ANTS tools

[brian avants]

hi everyone

this bug was identified a month or so ago ... i was never able to
reproduce but it occurred on some linux variant and was related to
pthreads.

the problem was fixed in v4.
 http://review.source.kitware.com/#/c/3610/

ants is undergoing a lot of refactoring @ the moment to make its
implementation more like a library.   ants also now has a superbuild
and so will download (or link to) all relevant code needed for its
compilation.   not sure if that's helpful.

brian





On Fri, Mar 9, 2012 at 10:04 AM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
> that is unfortunate -- it would take us a bit more time to figure it out
> -- primary complication is
>
> and that fresh ANTs development requires ITK4 which is still only in
> Debian experimental and still has issues (e.g. failing unittests)
> forbidding it even to build across architectures.
>
>
> Hi Brian,
>
> Am I dreaming up that when we met a few weeks ago you said it might be feasible
> to make current ANTs code compatible with ITK 3.2x through carrying
> necessary complimentary code which got into ITK 4.x?
>
>
> Antti,
>
> regarding:
>> Unfortunately it doesn't work even with the Normalize argument there.
>> Similar behaviour still.
>
> just out of curioucity --  is it a segfault again or something like
>
> Exception caught during reference file reading
>
> itk::ImageFileReaderException (0x16bfab0)
> Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 3u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
> File: /usr/include/InsightToolkit/IO/itkImageFileReader.txx
> Line: 146
> Description:  Could not create IO object for file /usr/lib/ants/AverageImages
> ...
> ?
>
>> Antti
>
>> to, 2012-03-08 kello 13:44 -0500, Yaroslav Halchenko kirjoitti:
>> > we both might have fell into RTFM trap ;)  or may be even more severe
>> > issue (I am not sure even if ANTS is building on wheezy ATM... so situation
>> > might vary).
>
>> > So:
>> > ,----------------------------------------------------------------------------------
>> > | $> /usr/lib/ants/AverageImages
>
>> > | Usage:
>
>> > | /usr/lib/ants/AverageImages ImageDimension Outputfname.nii.gz Normalize <images>
>> > `---
>
>> > mention that Normalize argument in there... so try
>
>> > AverageImages 3 out.nii.gz 0 *.nii.gz
>
>> > and please report back if that works for you :)
>
>> > > Hello!
>
>> > > I am trying to make a normalixed template with ANTS tools.When I run
>> > > AverageImages program I am getting segmentation fault.
>
>> > > AverageImages 3 out.nii.gz *.nii.gz
>> > >  Averaging 14 images
>> > >  fn ap_antsT1.nii.gz
>> > >  fn el_antsT1.nii.gz
>> > >  fn hn_antsT1.nii.gz
>> > >  fn hv_antsT1.nii.gz
>> > >  fn jh_antsT1.nii.gz
>> > >  fn jml_antsT1.nii.gz
>> > >  fn jp_antsT1.nii.gz
>> > >  fn jv_antsT1.nii.gz
>> > >  fn mh_antsT1.nii.gz
>> > >  fn mk_antsT1.nii.gz
>> > >  fn pv_antsT1.nii.gz
>> > >  fn rk_antsT1.nii.gz
>> > >  fn sk_antsT1.nii.gz
>> > >  fn sr_antsT1.nii.gz
>> > >  largest image [0, 0, 0]
>> > >  file AverageImages does not exist .
>> > > Segmentation fault
>
>> > > Anyone experiencing similar problems? This on Debian Wheezy (AMD64).
>
>> > > Greetings,
>
>> > > Antti
>
>
>> > > _______________________________________________
>> > > Neurodebian-users mailing list
>> > > Neurodebian-users at lists.alioth.debian.org
>> > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
>
>
>
>
>
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>
>
> --
> =------------------------------------------------------------------=
> Keep in touch                                     www.onerussian.com
> Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic