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

[Luis Ibanez]

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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