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

[Luis Ibanez]

Hi Xi,

Unfortunately, I'm not aware of any comprehensive document
describing the many file formats used in medical imaging.

                  You raise indeed a good point.

We should probably pursue the creation of such document.

One option is to use the ITK Wiki, and to ask experts on
each file format to provide information about them.

Most of what we currently know about file formats have been
learned the hard way. That is, mostly by error and trial, as
just happened to you with this image orientation problem.

Not to mention that for every file format you will have multiple
versions, as they change over the years.



     Regards


          Luis


-----------------------------------------------------------------------------
2010/2/15 Xi LIANG <liangxi1986317 at hotmail.com>:
> 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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