[Insight-users] masking part of an image

Sun Apr 19 21:45:17 EDT 2009

Hi, from your code, it seems that you forgot to allocate memory for your
output image.
try to add
outputImage->SetRegions(inputMaskImage->GetBufferedRegion());
outputImage->Allocate();

before the loop.

bill.lorensen at gmail.com,

2009/4/20 shoosh moosh <babygirl_25 at hotmail.com>

>  This is what I got when I printed them:
>
> Image (0x857c040)
>   RTTI typeinfo:   itk::Image<short, 3u>
>   Reference Count: 2
>   Modified Time: 205
>   Debug: Off
>   Observers:
>     none
>   Source: (0x8579948)
>   Source output index: 0
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 27
>   UpdateMTime: 206
>   LargestPossibleRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [540, 520, 720]
>   BufferedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [540, 520, 720]
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [540, 520, 720]
>   Spacing: [1, 1, 1]
>   Origin: [0, 0, 0]
>   Direction :
> 1 0 0
> 0 1 0
> 0 0 1
>
>   IndexToPointMatrix:
>   1 0 0
> 0 1 0
> 0 0 1
>
>   PointToIndexMatrix:
>   1 0 0
> 0 1 0
> 0 0 1
>
>   PixelContainer:
>     ImportImageContainer (0x857c1f8)
>       RTTI typeinfo:   itk::ImportImageContainer<unsigned long, short>
>       Reference Count: 1
>       Modified Time: 203
>       Debug: Off
>       Observers:
>         none
>       Pointer: 0x9fb12008
>       Container manages memory: true
>       Size: 202176000
>       Capacity: 202176000
> Image (0x857e938)
>   RTTI typeinfo:   itk::Image<unsigned char, 3u>
>   Reference Count: 2
>   Modified Time: 3 57
>   Debug: Off
>   Observers:
>     none
>   Source: (0x857c240)
>   Source output index: 0
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 28
>   UpdateMTime: 358
>   LargestPossibleRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [540, 520, 720]
>   BufferedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [540, 520, 720]
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [540, 520, 720]
>   Spacing: [1, 1, 1]
>   Origin: [0, 0, 0]
>   Direction:
> 1 0 0
> 0 1 0
> 0 0 1
>
>   IndexToPointMatrix:
>   1 0 0
> 0 1 0
> 0 0 1
>
>   PointToIndexMatrix:
>   1 0 0
> 0 1 0
> 0 0 1
>
>   Pi xelContainer:
>     ImportImageContainer (0x857eaf0)
>       RTTI typeinfo:   itk::ImportImageContainer<unsigned long, unsigned
> char>
>       Reference Count: 1
>       Modified Time: 355
>       Debug: Off
>       Observers:
>         none
>       Pointer: 0x93a42008
>       Container manages memory: true
>       Size: 202176000
>       Capacity: 202176000
>
> I think they are the same size, right? However one is a an image of short's
> while the other is of unsigned char's.
>
>
>
>
> > Date: Sun, 19 Apr 2009 15:35:53 -0400
> > Subject: Re: [Insight-users] masking part of an image
> > From: bill.lorensen at gmail.com
> > To: babygirl_25 at hotmail.com
> &g t; CC: insight-users at itk.org
>
> >
> > Are the input and input mask the same size? Try printing them.
> > inputImage->Print(std::cout);
> > inputMaskImage->Print(std::cout);
> >
> > after the Update's
> >
> > 2009/4/19 shoosh moosh <babygirl_25 at hotmail.com>:
> > > Ok, I added the reader->Update(), but now I'm getting a different
> error:
> > > Segmentation fault
> > >
> > > The program apparently crashes in the for loop.
> > >
> > > I think something might be wrong with lines 64-65, but I'm not sure
> what.
> > > inputImage=reader1->GetOutput();
> > > inputMaskImage=reader2->GetOutput();
> > >
> > > I attached the code again.
> > > Thanks
> > >
> > >
> > >
> > >> Date: Sun, 19 Apr 2009 14:57:47 -0400
> > >> Subject: Re: [Insight-users] masking part of an image
> > >> From: bill.lorensen at gmail.com
> > >> To: babygirl_25 at hotmail.com
> > >> CC: insight-users at itk.org
> > >>
> > >> Do a reader1->Update() and reader2->Update() before accessing the
> > >> outputs of the reader.
> > >>
> > >> 2009/4/19 shoosh moosh <babygirl_25 at hotmail.com>:
> > >> > Hi,
> > >> > I wrote up a program that takes as input 2 images - a 3D image, and
> a 3D
> > >> > binary mask image with 0's in the parts im not interested and 1's in
> the
> > >> > parts I want to segment out. I want the program to simply multiply
> each
> > >> > pixel in the original image with the corresponding pixel in the
> masking
> > >> > image and produce a third image of the same size having only the
> region
> > >> > specified by 1's in the mask. The code compiles, but when I run it,
> I
> > >> > get
> > >> > this error:
> > >> & gt;
> > >> > terminate called after throwing an instance of
> 'itk::ExceptionObject'
> > >> >   what():
> > >> > /home/shoosh/InsightToolkit-3.10.2/Code/IO/itkNrrdImageIO.cxx:951:
> > >> > itk::ERROR: NrrdImageIO(0x8585a50): Write: Error wrapping nrrd for
> > >> > output.nhdr:
> > >> > [nrrd] nrrdWrap_nva:
> > >> > [nrrd] _nrrdSizeCheck: axis 0 size is zero!
> > >> >
> > >> > Can some one tell me how to fix it. the code is attached.
> > >> >
> > >> >
> > >> >
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