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

Xi LIANG liangxi1986317 at hotmail.com
Mon Feb 15 18:43:51 EST 2010 

Dear Luis,
Thank you very much for this. Finally I realize the format is a big issue for image processing, and this has been confusing me a lot. Could you please suggest a good reference for understanding and analysis on format and head file information, which could show the important parameters that would effect the result significant and how.  
I will post some later if I manage to find any good reference.
Thank you and regards,

--------------------------------
Xi Liang

梁茜
--------------------------------




> Date: Mon, 15 Feb 2010 18:08:32 -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,
> 
> 
>          That explains everything    :-)
> 
> 
> Analyze can only manage some orientations
> (only three actually), and the Identity matrix is
> not one of them, so it seems to be defaulting
> to one of the directions that it actually supports.
> 
> 
> Please don't use the Analyze fileformat.
> 
> 
> You may want to use
> 
>               * MetaImage  (extension ".mha") or
>               * Nifti (extension   ".nii" )
> 
> 
>     Regards
> 
> 
>              Luis
> 
> 
> 
> ---------------------------------------------------------------------
> 2010/2/15 Xi LIANG <liangxi1986317 at hotmail.com>:
> > 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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