[Insight-users] Problem in reading nifti image

[Luis Ibanez]

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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