[ITK] Reading 4D Nifti into a 3D Vector Image

[Wood, Tobias]

Dear Matt and Brad,
Thanks for the quick response. The approach you suggested sounds good, so I gave it a try using itk::VectorImage<float, 3> and itk::ImageFileReader. However, this appears to read 4D niftis as only having 1 component (using the GetNumberOfComponentsPerPixel() method). I confirmed this by compiling the example at http://www.itk.org/Wiki/ITK/Examples/IO/ReadVectorImage and running it with multiple files that I have - it reported each one as having only 1 component.

Is this to do with the choice of nifti format? Technically, vector images are supposed to use the 5th dimension as the vector length in nifti, not the 4th.

Thanks,
Tobias

________________________________________
From: Matt McCormick <matt.mccormick at kitware.com>
Sent: 12 January 2015 17:24
To: Wood, Tobias
Cc: community at itk.org
Subject: Re: [ITK] Reading 4D Nifti into a 3D Vector Image

Hi Tobias,

For this case, it may be better to read in the image as an

  itk::Image< itk::Vector< float, NumberOfComponents >, 3 >

or

  itk::VectorImage< float, 3 >

HTH,
Matt

On Mon, Jan 12, 2015 at 11:33 AM, Wood, Tobias <tobias.wood at kcl.ac.uk> wrote:
> Hello,
>
> I am new to ITK and am working with datasets that are stored as 4D niftis of
> variable length in the 4th dimension. The algorithm I need to write takes
> the "vector" stored in the 4th dimension as input at each voxel, and
> produces some scalar values as output. I would like to write a filter to
> contain this algorithm, but I am struggling to work out how to specify the
> input and iterate efficiently over it.
>
>
> My output image type is itk::Image<float, 3>. I assume that my input image
> type should be itk::Image<float, 4>. Inside the filter, I was planning on
> using ImageRegionIterator with GetLargestPossibleRegion() to iterate over
> the output voxels.
>
>
> Is there a suitable iterator and region to obtain the vector of values for
> each input voxel efficiently? Or, alternatively, is there another approach
> that I should be taking? Perhaps using another filter to convert the input
> data first?
>
>
> Thanks in advance and I hope my question is clear,
>
> Tobias Wood
>
>
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