[Insight-users] Segmentation Faults with ITK

[Karsten Grasemann]

Hello everybody,

I have a big problem with itk. I try to build an application that can do some
segmentation an generates a model out of a DICOM or RAW-Image.
So I implement the example from the "ItkSoftwareGuide, Chapter 9.4.3
Deformable Model and Gibbs Prior" in a seperate method. Another method will
build my binary-image as described in Chapter 9.1.1 "Connected Threshold".
Everything is wrapped in a Qt-GUI framework.

So far so good. In the compilation process I get some warnings :
"...
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx: In
   member function `typename itk::FiniteDifferenceFunction<TImage>::PixelType
   itk::CurvatureFlowFunction<TImage>::ComputeUpdate(typename
   itk::FiniteDifferenceFunction<TImageType>::NeighborhoodType&, void*,
   typename itk::FiniteDifferenceFunction<TImageType>::FloatOffsetType&) [with
   TImage = itk::Image<short unsigned int, 3>]':
/usr/local/include/InsightToolkit/Common/itkPointLocator.txx:161:
instantiated from here
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:104:
Warnung: initialization
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:104:
Warnung: argument
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Common/itkPointLocator.txx:161:
instantiated from here
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:109:
Warnung: assignment
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:109:
Warnung: argument
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Common/itkPointLocator.txx:161:
instantiated from here
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:119:
Warnung: assignment
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:119:
Warnung: argument
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:137:
Warnung: initialization
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:137:
Warnung: argument
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Common/itkPointLocator.txx:161:
instantiated from here
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:143:
Warnung: assignment
    to `short unsigned int' from `double'
/usr/local/include/InsightToolkit/Algorithms/itkCurvatureFlowFunction.txx:143:
Warnung: argument
    to `short unsigned int' from `double'
... "

... nothing serious so far. But when I run the application, my program bails
out with a segmentation fault in the calculation of the Deformable Mesh
Filter.
So I started a new Gdb-session and got the following Debug Infos:

"...
Using host libthread_db library "/lib/tls/libthread_db.so.1".
(gdb) set args
(gdb) run
[Thread debugging using libthread_db enabled]
[New Thread 1086799200 (LWP 10627)]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 1086799200 (LWP 10627)]
itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin (this=0x0) at stl_iterator.h:593
(gdb)

..."

an assembler dump does the following

"...

Dump of assembler code for function
_ZN3itk15VectorContainerImPNS_13CellInterfaceIdNS_14CellTraitsInfoILi3EffmmmNS_5PointIfLj3EEENS0_ImS4_EESt3setImSt4lessImESaImEEEEEEE5BeginEv:
    0x080f8570 <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+0>:   push   %ebp
    0x080f8571 <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+1>:   mov    %esp,%ebp
    0x080f8573 <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+3>:   mov    0xc(%ebp),%edx
    0x080f8576 <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+6>:   mov    0x8(%ebp),%eax

-- Here comes the Point of bailout -->    0x080f8579
<itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+9>:   mov    0x30(%edx),%edx
    0x080f857c <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+12>:  movl   $0x0,(%eax)
    0x080f8582 <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+18>:  mov    %edx,0x4(%eax)
    0x080f8585 <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+21>:  pop    %ebp
    0x080f8586 <itk::VectorContainer<unsigned long, itk::CellInterface<double,
itk::CellTraitsInfo<3, float, float, unsigned long, unsigned long, unsigned
long, itk::Point<float, 3u>, itk::VectorContainer<unsigned long,
itk::Point<float, 3u> >, std::set<unsigned long, std::less<unsigned long>,
std::allocator<unsigned long> > > >*>::Begin()+22>:  ret    $0x4
End of assembler dump.
..."

it seems to come out of the stdlib

"
template<typename _Iterator, typename _Container>
 574     class __normal_iterator
 575       : public iterator<typename
iterator_traits<_Iterator>::iterator_category,
 576                         typename iterator_traits<_Iterator>::value_type,
 577                         typename
iterator_traits<_Iterator>::difference_type,
 578                         typename iterator_traits<_Iterator>::pointer,
 579                         typename iterator_traits<_Iterator>::reference>
 580     {
 581     protected:
 582       _Iterator _M_current;
 583
 584     public:
 585       typedef typename iterator_traits<_Iterator>::difference_type
 586
difference_type;
 587       typedef typename iterator_traits<_Iterator>::reference   reference;
 588       typedef typename iterator_traits<_Iterator>::pointer     pointer;
 589
 590       __normal_iterator() : _M_current(_Iterator()) { }
 591
 592       explicit
--- Bailout here --->
 593       __normal_iterator(const _Iterator& __i) : _M_current(__i) { }
 594
 595       // Allow iterator to const_iterator conversion
 596       template<typename _Iter>
 597       inline __normal_iterator(const __normal_iterator<_Iter,
_Container>& __i)
 598         : _M_current(__i.base()) { }
 599

"

So, has anybody an idea of a workaround ? Even the examples in the
InsightApplications will bail out with a segmentation fault. I haven't
debugged them yet ...

Some system and version infos:
AMD 2200+, 512Meg, SuSE-Linux-i586 2.6.5, GCC 3.3.3-41, CMake 2.0.5,
InsightToolkit 1.8.0, InsightApplications 1.8.0, VTK 4.2, QT 3.3.1-36.16, DDD
3.3.8

Thanx for the help

Karsten Grasemann