[Insight-users] Problem in reading nifti image

Fri Mar 25 21:44:20 EDT 2011

HI, Michael
      If your output image is the last selectorIndex component of input
vectorimage, you might need disconnect the output image before proceed on.
See embedded lines.

On Sat, Mar 26, 2011 at 1:50 AM, Hsieh <M.Hsieh at student.tudelft.nl> wrote:

> Hi Luis,
>
> This is a very helpful message that this filter does exactly what I need.
>
> But, I am wondering if I can use only one instance of the filter to
> generate multiple output by setting different index? I've tried something as
> below,
>  int selectorIndex = 0;
>  selector->SetIndex( selectorIndex );
>
 selector->Update();
ScalarImagePointer output0 = selector->GetOutput();
output0->DisconnectPipeline();

>  writer0->SetInput( output0);
>  selectorIndex++;
>
>  selector->SetIndex( selectorIndex );
>
  selector->Update();
ScalarImagePointer output1 = selector->GetOutput();
output1->DisconnectPipeline();

>  writer1->SetInput( output1);
>  selectorIndex++;
>
> and so on. But all the writers give the same component of the tensor image.
> Instead, I have to instantiate 6 selectors as many as the writers to achieve
> the goal of saving six components of a DTI tensor image.
> However, I'd like to have a single class and one instance that can produce
> multiple outputs, say, extract all six components in the tensor like:
>        selector->GetComponentOne( );
>        selector->GetComponentTwo( );
> and so on.
> Do you think that I have to write a new class capable of multiple outputs
> inherited from the itkVectorIndexSelectionCastImageFilter? Or any simpler
> way?
>
>
>
> Best regards,
> Meng-Kang Hsieh (Michael)
>
>
> -----Original Message-----
> From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Sent: Tuesday, February 22, 2011 12:54 AM
> To: robert tamburo
> Cc: Hsieh; insight-users at itk.org; norman-k-williams at uiowa.edu
> Subject: Re: [Insight-users] Problem in reading nifti image
>
> Hi Michael
>
> As Robert described, the ImageAdaptor will not work before a Writer.
>
> You may want to use instead the filter:
>
>
> http://public.kitware.com/Insight/Doxygen/html/classitk_1_1VectorIndexSelectionCastImageFilter.html
>
>
>     Luis
>
>
> ---------------------------------
> On Mon, Feb 21, 2011 at 2:06 PM, robert tamburo
> <robert.tamburo at gmail.com> wrote:
> > Section 12.5 of the ITK software guide:
> > 12.5 Adaptors and Writers
> > Image adaptors will not behave correctly when connected directly to a
> > writer. The reason is
> > that writers tend to get direct access to the image buffer from their
> input,
> > since image adaptors
> > do not have a real buffer their behavior in this circumstances is
> incorrect.
> > You should avoid
> > instantiating the ImageFileWriter or the ImageSeriesWriter over an image
> > adaptor type.
> > From an email to the user list by Luis'
> > (http://www.itk.org/pipermail/insight-users/2005-April/012553.html):
> > This means that when you use ImageAdaptors, you must make sure
> > that the filter receiving the Adaptor is based on the use of the
> > "*WithIndex" iterators.
> >
> > On Mon, Feb 21, 2011 at 1:36 PM, Hsieh <M.Hsieh at student.tudelft.nl>
> wrote:
> >>
> >> Hi,
> >>
> >>
> >>
> >> Now I send it to Insight-Users mailing list.
> >>
> >> My purpose is to extract elements from the tensor image to analyze and
> >> register the tensor channels. With your help now I can do so with vector
> >> image adaptor, which extracts one of the element of the vector. However,
> in
> >> the example of ImageAdaptor3.cxx, the adaptor itself cannot directly be
> fed
> >> into the writer to create a scalar image. It is shown that a filter,
> such as
> >> rescaling the intensity, has to be done and therefore the
> >> rescaler->GetOutput() can be set as the input image for writer. Is there
> a
> >> way not to modify the intensity of the image? Is there an identity
> filter or
> >> something like that?
> >>
> >>
> >>
> >> Best regards,
> >>
> >> Michael
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> This is more of a question for the Insight-Users mailing list.
> >>
> >>
> >>
> >> That being said, you don't show your work, so I can't say exactly what
> >> you're doing wrong.
> >>
> >>
> >>
> >> I wrote the NIfTI image reader, and as I remember there's some strange
> >> things that go on with respect to  Images with dimension > 3.
> >>
> >>
> >>
> >> If I recall correctly, in a NIfTI image dimensions of [ 128 128 64 1 6 ]
> >> would not correspond to an 5D scalar image at all.  It would be a 3D
> image
> >> where each voxel is a 6-element vector.  The 4th dimension is ALWAYS
> >> interpreted as a time dimension, and the sixth and subsequent dimensions
> are
> >> interpreted according to what the image modality actually was.  Most
> often,
> >> and what's implemented in the reader, is to interpret it as an Image of
> >> Vector voxels. So NiftiImageIO reads in 6 3D volumes, and then
> constructs
> >> vector pixels by pulling one pixel from each of the volumes.
> >>
> >>
> >>
> >> In other words if you used
> >>
> >>
> >>
> >> typedef itk::Image< itk::Vector<float, 6>, 3 > ImageType;
> >>
> >> typedef itk::ImageFileReader<Imagetype> ImageReaderType;
> >>
> >>
> >>
> >> You would get all the data.  If you use
> >>
> >>
> >>
> >> typedef itk::Image<float, 3> ImageType;
> >>
> >> typedef itk::ImageFileReader<ImageType> ImageReaderType;
> >>
> >>
> >>
> >> the ImageFileReader will think that it's a vector image and try to
> convert
> >> the vector voxels to a scalar voxel, probably by taking the first value
> of
> >> each voxel's vector.  It will then report the image size as you
> reported.
> >>
> >>
> >>
> >> From: Hsieh <M.Hsieh at student.tudelft.nl>
> >> Date: Fri, 18 Feb 2011 16:35:07 +0100
> >> To: ITK <insight-developers at itk.org>
> >> Subject: [Insight-developers] Problem in reading 5D nifti image
> >>
> >>
> >>
> >> Hi,
> >>
> >>
> >>
> >> I am trying to read a diffusion tensor image in nifti(.nii) format,
> which
> >> has dimension of [128 128 64 1 6]. However, the image I got after read
> by
> >> the itkImageFileReader.h had dimension only [128 128 64 1 1]. The last
> two
> >> dimension are suppressed by the reader. When I looked into the class
> (.h)
> >> and the .txx file, I found out that the numberOfDimensionsIO, which is
> 3, is
> >> smaller than TOutputImage::ImageDimension, which is set manually to 5,
> so
> >> that the 4th and the 5th dimension are set to 1 later. Why does that
> happen?
> >> numberOfDimensionsIO should be 5 in this case.
> >>
> >>
> >>
> >> Best regards,
> >>
> >> Meng-Kang Hsieh (Michael)
> >>
> >> OpSciTech, Erasmus Mundus
> >>
> >> Delft University of Technology
> >>
> >>
> >>
> >>
> >>
> >> Best regards,
> >>
> >> Meng-Kang Hsieh (Michael)
> >>
> >> OpSciTech, Erasmus Mundus
> >>
> >> Delft University of Technology
> >>
> >>
> >>
> >>
> >>
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> >
> >
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>
> Visit other Kitware open-source projects at
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>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
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