[Neurodebian-users] Seg fault with atlasquery

[Yaroslav Halchenko]

On Thu, 09 Jan 2014, Jonathan Brooks wrote:

> Here you go….

> $ sudo apt-cache policy libnifti2

> libnifti2:
>   Installed: 2.0.0-1
>   Candidate: 2.0.0-1
>   Version table:
>  *** 2.0.0-1 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
>         100 /var/lib/dpkg/status

> Does that match other installed versions?

yeap

good news -- could reproduce in precise chroot

bad news -- would need more troubleshooting (by me or anyone else) etc

next suspect is the actual zlib1g which is quite aged in 12.04:
1:1.2.3.4.dfsg-3ubuntu4 as opposed to e.g. 1:1.2.7.dfsg-13 in Debian
wheezy.  upstream's changelog of fixes between the two is quite long.

reason: valgrind complaints:

==3955== Conditional jump or move depends on uninitialised value(s)
==3955==    at 0x76844E0: inflateReset2 (in /lib/x86_64-linux-gnu/libz.so.1.2.3.4)
==3955==    by 0x76845D8: inflateInit2_ (in /lib/x86_64-linux-gnu/libz.so.1.2.3.4)
==3955==    by 0x767E323: ??? (in /lib/x86_64-linux-gnu/libz.so.1.2.3.4)
==3955==    by 0x52AC238: znzopen (in /usr/lib/libznz.so.2.0.0)
==3955==    by 0x5092CE4: nifti_fileexists (in /usr/lib/libniftiio.so.2.0.0)
==3955==    by 0x50932C9: nifti_findhdrname (in /usr/lib/libniftiio.so.2.0.0)
==3955==    by 0x47E17D: FslFileExists (in /usr/bin/atlasquery)
==3955==    by 0x482EFC: FslXOpen (in /usr/bin/atlasquery)
==3955==    by 0x44C47A: Image::Image(std::string const&) (in /usr/bin/atlasquery)
==3955==    by 0x44C9DD: Image::load(std::string const&, bool) (in /usr/bin/atlasquery)
==3955==    by 0x4342E1: readImage(std::string const&, QDomNode&, std::string const&) (in /usr/bin/atlasquery)
==3955==    by 0x4366C6: FileManager::readXMLAtlas(std::string const&, std::string const&) (in /usr/bin/atlasquery)

I am not sure if that would be safe to just provide a backport (someone
would need to check if API/ABI hasn't changed etc).

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik