[Insight-users] fail to change the Direction Cosine Matrix to identity

Xi LIANG liangxi1986317 at hotmail.com
Mon Feb 15 18:05:15 EST 2010 

Hi Luis,

> What file format are you using for storing the images ?> > That is, what is the extension of the filename that you> are passing as the second command line argument to> your program ?
I am using .hdr
Regards,
--------------------------------
Xi Liang

梁茜
--------------------------------




> Date: Mon, 15 Feb 2010 18:04:09 -0500
> Subject: Re: [Insight-users] fail to change the Direction Cosine Matrix to 	identity
> From: luis.ibanez at kitware.com
> To: liangxi1986317 at hotmail.com
> CC: insight-users at itk.org; m.staring at lumc.nl; njuptlw at 163.com
> 
> Hi Xi,
> 
> 
> The problem seems to be in the writer / reader that
> is used for the writing and reading the changed image.
> 
> 
> What file format are you using for storing the images ?
> 
> That is, what is the extension of the filename that you
> are passing as the second command line argument to
> your program ?
> 
> 
>      Please let  us know,
> 
> 
>            Thanks
> 
> 
>                   Luis
> 
> 
> ------------------------------------------------------------------------------------------
> 2010/2/15 Xi LIANG <liangxi1986317 at hotmail.com>:
> > Hi all,
> > I wrote 2 pieces of code to change the direction to identity. The idea of
> > the program is to read in the input image and only change its direction, and
> > then write the resulting image into output. Those code is attached with the
> > email.
> >
> > However, both of them cannot change the direction to identity and generate
> > the same unrelated directions. One method is
> > though itkChangeInformationImageFilter suggested by Luis, and the other is
> > using ResampleImageFilter suggested by another ITK user.
> >
> > By using those two methods, I got the same wired result. The direction of
> > the output image is different from input image direction and is not identity
> > direction neither. I am not sure why the direction in the filter is
> > identity, but it generates a totally unrelated direction in writer. The
> > followings are direction shows the directions in Input/filter/output
> > images.
> >
> > Input image DCM:
> > 1 0 0
> > 0 -1 0
> > 0 0 1
> > DCM got from the filter
> > 1 0 0
> > 0 1 0
> > 0 0 1
> > Output image DCM:
> > 1 0 0
> > 0 0 -1
> > 0 1 0
> > --------------------------------
> > Xi Liang
> >
> > 梁茜
> > --------------------------------
> >
> >
> >
> >
> >> Date: Fri, 12 Feb 2010 09:03:51 -0500
> >> Subject: Re: [Insight-users] fail to change the Direction Cosine Matrix to
> >> identity
> >> From: luis.ibanez at kitware.com
> >> To: liangxi1986317 at hotmail.com
> >> CC: insight-users at itk.org
> >>
> >> Hi Xi,
> >>
> >> You should not attempt to modify directly the information of an
> >> image that is generated as the output of a filter (or a reader).
> >>
> >>
> >> What you should do, is to use the
> >>
> >> itkChangeInformationImageFilter
> >>
> >>
> >> Connect this filter to the output of the reader and make sure
> >> that you call ChangeDirectionOn() in the filter before you
> >> call Update()
> >>
> >>
> >> BTW: changing the direction of a medical image can
> >> be a dangerous thing to do. You should make sure
> >> that you have a good justification for replacing the
> >> direction of the original image.
> >>
> >>
> >>
> >> Regards,
> >>
> >>
> >>
> >> Luis
> >>
> >>
> >> -------------------------------------------------------------------
> >> 2010/2/12 Xi LIANG <liangxi1986317 at hotmail.com>:
> >> > Dear all,
> >> > I am trying to change an image direction cosine matrix to identity by
> >> > using
> >> > the following code, but it fails. I read in an input image and set its
> >> > DCM
> >> > to identity, then I write it to a new image and then print out its DCM
> >> > again. However, the DCM in the new image is not identity matrix. I am
> >> > not
> >> > sure what was wrong in my code, and the following are the major part
> >> > related
> >> > to this.
> >> >
> >> > // I first get the DCM from the fixedImage
> >> > FixedImageType::DirectionType directionCosines =
> >> > fixedImage->GetDirection();
> >> >
> >> > std::cout << "Input DCM is " << std::endl;
> >> > std::cout << directionCosines << std::endl;
> >> > //Terminal shows:
> >> > //1 0 0
> >> > //0 -1 0
> >> > //0 0 1
> >> > directionCosines[0][0] = 1;
> >> > directionCosines[0][1] = 0;
> >> > directionCosines[0][2] = 0;
> >> > directionCosines[1][0] = 0;
> >> > directionCosines[1][1] = 1;
> >> > directionCosines[1][2] = 0;
> >> > directionCosines[2][0] = 0;
> >> > directionCosines[2][1] = 0;
> >> > directionCosines[2][2] = 1;
> >> > std::cout << directionCosines << std::endl;
> >> > //Terminal shows:
> >> > //1 0 0
> >> > //0 1 0
> >> > //0 0 1
> >> >
> >> > //Then I reset the direction to identity
> >> > fixedImage Reader->GetOutput()->SetDirection(directionCosines);
> >> >
> >> > std::cout << "New DCM is " << std::endl;
> >> > std::cout << fixedImageReader->GetOutput()->GetDirection() << std::endl;
> >> > //Terminal shows:
> >> > //1 0 0
> >> > //0 1 0
> >> > //0 0 1
> >> >
> >> >
> >> > //Then I write the new image with the identity DCM
> >> > caster->SetInput( fixedImageReader->GetOutput() );
> >> > &nbsp ; writer->SetInput( caster->GetOutput() );
> >> >
> >> > //Then I read in the new image again to print its DCM
> >> > outputImageReader->SetFileName( argv[2] );
> >> > OutputImageType::ConstPointer outputImage =
> >> > outputImageReader->GetOutput();
> >> > outputImageReader->Update();
> >> > OutputImageType::DirectionType directionCosinesOutput =
> >> > outputImage->GetDirection();
> >> > std::cout << "Output DCM is " << std::endl;
> >> > std::cout << directionCosinesOutput << std::endl;
> >> > //Terminal shows:
> >> > //1 0 0
> >> > // 0 -1 0
> >> > //0 0 1
> >> > --------------------------------
> >> > Xi Liang
> >> >
> >> > 梁茜
> >> > --------------------------------
> >> >
> >> >
> >> >
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