[Insight-users] masking part of an image

shoosh moosh babygirl_25 at hotmail.com
Mon Apr 20 11:14:10 EDT 2009 

Thanks!!! You're absolutely right. But it should be 
outputImage->SetRegions(inputImage->GetBufferedRegion()); 
instead of
outputImage->SetRegions(inputMaskImage->GetBufferedRegion());
because inputImage is the one like the outputImage not inputMaskImage..
Thanks a lot.


Date: Mon, 20 Apr 2009 11:45:17 +1000
Subject: Re: [Insight-users] masking part of an image
From: nadan.zhu at gmail.com
To: babygirl_25 at hotmail.com
CC: insight-users at itk.org

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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