[Insight-users] Vital DICOM information/tags when registering images?
Patrik Brynolfsson
patrik.brynolfsson at gmail.com
Wed Sep 16 09:27:20 EDT 2009
Hello Andriy,
thanks for you tips. I reinitialize the seed every time, so the two
different methods are consistent between runs but not between each other.
I'm checking if the two different methods of reading the images result in
the same pixel values right now, so I will report back on that when I have
the results. The difference between the methods are huge for some images,
and reading the images from files constantly generate correct results
whereas the resuts when the images are passed from matlab are sometimes
really bad (rotated 90 degrees or something like that).
I was thinking of comparing the images using an iterator and comparing pixel
by pixel. Is there another way of comparing the images that is easier?
Thanx for your input.
//Patrik
2009/9/16 Andriy Fedorov <fedorov at bwh.harvard.edu>
> Patrick,
>
> Registration has the metric sampling component, which is initialized
> with a random seed by default. If you want to have consistent results
> you might need to initialize registration with the same seed.
>
> Another guess is to check that there is no type cast involved when you
> read the image in Matlab. This might result in loss of precision.
>
> Not sure if any of these is the source of the problem for you, just
> some ideas to investigate.
>
> Andriy Fedorov
>
>
>
> > Date: Wed, 16 Sep 2009 09:02:59 +0200
> > From: Patrik Brynolfsson <patrik.brynolfsson at gmail.com>
> > Subject: Re: [Insight-users] Vital DICOM information/tags when
> > registering images?
> > To: Bill Lorensen <bill.lorensen at gmail.com>, ITK
> > <insight-users at itk.org>
> > Message-ID:
> > <8d0068770909160002r1e0aa86el32f78b0d027c9368 at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hello Bill, thanx for answering!
> >
> > The filter I use are:
> > Registration part (same for both cases):
> >
> > itkImageRegistrationMethod
> > itkMattesMutualInformationImageToImageMetric
> > itkLinearInterpolateImageFunction
> > itkVersorRigid3DTransform
> > itkVersorRigid3DTransformOptimizer
> > itkCenteredTransformInitializer
> >
> > Reading images from memory:
> >
> > itkImportImageFilter
> > itkChangeInformationImageFilter
> >
> > Reading images from DICOM:
> >
> > itkImageSeriesReader
> > itkGDCMImageIO
> > itkGDCMSeriesFileNames
> >
> > *The code to read images from memory is:*
> >
> > typedef itk::ImportImageFilter<PixelType,Dimension> ImportFilterType;
> > ImportFilterType::Pointer fixedImageReader = ImportFilterType::New();
> > ImportFilterType::Pointer movingImageReader = ImportFilterType::New();
> >
> > const mwSize* dimsFix = mxGetDimensions(prhs[0]);
> > const mwSize* dimsMov = mxGetDimensions(prhs[1]);
> >
> > ImportFilterType::SizeType sizeFix;
> > ImportFilterType::SizeType sizeMov;
> > sizeFix[0] = dimsFix[0];
> > sizeFix[1] = dimsFix[1];
> > sizeFix[2] = dimsFix[2];
> >
> > sizeMov[0] = dimsMov[0];
> > sizeMov[1] = dimsMov[1];
> > sizeMov[2] = dimsMov[2];
> >
> > ImportFilterType::IndexType start;
> > start.Fill( 0 );
> > ImportFilterType::RegionType regionFix;
> > regionFix.SetIndex( start );
> > regionFix.SetSize( sizeFix );
> > ImportFilterType::RegionType regionMov;
> > regionMov.SetIndex( start );
> > regionMov.SetSize( sizeMov );
> > fixedImageReader->SetRegion( regionFix );
> > movingImageReader->SetRegion(regionMov );
> >
> > //Import image from memory, passed from MATLAB
> >
> fixedImageReader->SetImportPointer((PixelType*)mxGetData(prhs[0]),mxGetNumberOfElements(prhs[0]),false);
> >
> movingImageReader->SetImportPointer((PixelType*)mxGetData(prhs[1]),mxGetNumberOfElements(prhs[1]),false);
> > fixedImageReader->Update();
> > movingImageReader->Update();
> >
> > *...and the code to set the relevant info is:*
> >
> > double *fixedSpacingInput = mxGetPr(prhs[2]);
> > double *movingSpacingInput = mxGetPr(prhs[3]);
> >
> > double *fixedOrientationInput = mxGetPr(prhs[4]);
> > double *movingOrientationInput = mxGetPr(prhs[5]);
> >
> > double *fixedOriginInput = mxGetPr(prhs[6]);
> > double *movingOriginInput = mxGetPr(prhs[7]);
> >
> > **Code for casting input to correct types are skipped, not important for
> > this question**
> >
> > typedef itk::ChangeInformationImageFilter< FixedImageType >
> > ChangeInfoType;
> > ChangeInfoType::Pointer changeFixedInfo = ChangeInfoType::New();
> > ChangeInfoType::Pointer changeMovingInfo = ChangeInfoType::New();
> >
> > changeFixedInfo->SetInput(fixedImageReader->GetOutput());
> > changeMovingInfo->SetInput(movingImageReader->GetOutput());
> >
> > changeFixedInfo->SetOutputSpacing(fixedSpacing);
> > changeMovingInfo->SetOutputSpacing(movingSpacing);
> > changeFixedInfo->SetChangeSpacing(true);
> > changeMovingInfo->SetChangeSpacing(true);
> >
> > changeFixedInfo->SetOutputDirection(fixedOrientation);
> > changeMovingInfo->SetOutputDirection(movingOrientation);
> > changeFixedInfo->SetChangeDirection(true);
> > changeMovingInfo->SetChangeDirection(true);
> >
> > changeFixedInfo->SetOutputOrigin(fixedOrigin);
> > changeMovingInfo->SetOutputOrigin(movingOrigin);
> > changeFixedInfo->SetChangeOrigin(true);
> > changeMovingInfo->SetChangeOrigin(true);
> >
> > changeFixedInfo->Update();
> > changeMovingInfo->Update();
> >
> > registration->SetFixedImage( changeFixedInfo->GetOutput() );
> > registration->SetMovingImage( changeMovingInfo->GetOutput() );
> > registration->SetFixedImageRegion(
> > changeFixedInfo->GetOutput()->GetBufferedRegion()
> > );
> >
> > As a check I print the origin, spacing and direction for the images and
> they
> > are identical to when reading from DICOM files. I read the DICOM series
> just
> > as described in chapter 7.12 in the ITK manual.
> >
> > Any ideas to what might be wrong here?
> >
> > Thanks in advance!
> >
> > //Patrik Brynolfsson
> >
> >
> >
> > 2009/9/16 Bill Lorensen <bill.lorensen at gmail.com>
> >
> >> You should get the same answers. Exactly what filters are you using in
> >> each of the cases. I can't tell from your description.
> >>
> >> Bill
> >>
> >> On Tue, Sep 15, 2009 at 4:38 PM, Patrik Brynolfsson
> >> <patrik.brynolfsson at gmail.com> wrote:
> >> > Hello,
> >> > I'm working on a Matlab mex-implementation of an ITK registration.
> This
> >> > means that instead of loading the images from files I will load them
> from
> >> > memory as 3D matrices. All the DICOM information needs to be passed to
> >> ITK
> >> > from Matlab as well, and this is where my problems begin. The
> information
> >> > that I thought was essential for a correct registration is:
> >> > * Origin
> >> > * Spacing
> >> > * Direction
> >> > I set these using the "ChangeInformationImageFilter" and it is
> working;
> >> the
> >> > images have the origin, spacing and directional cosines that are
> assigned
> >> to
> >> > them, and they are the same as if the dicom images were loaded from
> >> files.
> >> > However, the result of the registration is different from that when
> >> loading
> >> > the images from files, with all other components set the same, (of
> course
> >> I
> >> > reinitialize the seed). Not by much, but they should be exactly the
> same!
> >> I
> >> > use Mattes mutual information metric, linear interpolation, Versor
> rigid
> >> 3D
> >> > transform and the accompanying Versor rigid 3D optimizer together with
> >> the
> >> > "CenteredTransformInitializer".
> >> > I know that the difference in results are due to the way I read the
> data.
> >> If
> >> > I change the input from memory to reading the dicom files I get the
> same
> >> > result as with a stand-alone .exe-application, so this is where the
> error
> >> > is.
> >> > Does anyone have any idea as to what other information I need to pass
> >> from
> >> > matlab to get identical results?
> >> > Thanks in advance
> >> > --
> >> > Patrik Brynolfsson
> >> >
> >> >
> >> >
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> >
> >
> >
> > --
> > Patrik Brynolfsson
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--
Patrik Brynolfsson
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