[Insight-users] Vital DICOM information/tags when registering images?
Patrik Brynolfsson
patrik.brynolfsson at gmail.com
Wed Sep 16 10:36:27 EDT 2009
Exelent, I will check that out!
2009/9/16 Bill Lorensen <bill.lorensen at gmail.com>
> Matlab stores images in Fortran (column) order. C/C++ in row order.
> This may account for the 90 degree difference.
>
> On Wed, Sep 16, 2009 at 9:27 AM, Patrik Brynolfsson
> <patrik.brynolfsson at gmail.com> wrote:
> > 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
> >> >> >
> >> >> >
> >> >> >
> >> >> > _____________________________________
> >> >> > Powered by www.kitware.com
> >> >> >
> >> >> > Visit other Kitware open-source projects at
> >> >> > http://www.kitware.com/opensource/opensource.html
> >> >> >
> >> >> > Please keep messages on-topic and check the ITK FAQ at:
> >> >> > http://www.itk.org/Wiki/ITK_FAQ
> >> >> >
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> >> >> > http://www.itk.org/mailman/listinfo/insight-users
> >> >> >
> >> >> >
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Patrik Brynolfsson
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> >
> >
> >
> > --
> > Patrik Brynolfsson
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
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> >
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>
--
Patrik Brynolfsson
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