[Insight-users] DiffusionTensor3DReconstructionFilter

[Karthik Krishnan]

On Mon, Feb 21, 2011 at 2:01 PM, alba garin <albagarin1986 at hotmail.com>wrote:

>
> Hello,
>
> I tried to use the code of the example of gtract and it happened the same,
> it takes correctly the gradients but when applying the filter,
> DiffusionTensor3DReconstructionImageFilter, it did not create the tensor
> correctly. I checked that because i read the positions of the tensor and
> everything i get is 0.00000 and it happened the same after computing the
> eigenvalues and eigenvectors of the tensor.
> I already have taken a look in the software guide, examples of itk, and
> every single example that appears on the internet.
>

Alba:

To restate, did you look at this specific example, I post below. The class
is tested you know at itkDiffusionTensor3DReconstructionImageFilterTest :



Also take a look at the examples and tests I placed in the repository:

   Examples/Filtering/DiffusionTensor3DReconstructionImageFilter.cxx


As the example mentions:

// The easiest way to get started is to try out the filter on a sample
dataset.
//
// Acquiring sample datasets:
//  1. Get the DWI datasets from
  http://public.kitware.com/pub/itk/Data/DTI/RawData/dwi.nhdr
  http://public.kitware.com/pub/itk/Data/DTI/RawData/dwi.img.gz
//     These datasets contain a reference T1 image and 30 diffusion weighted
//     images. See the nrrd header for details such as B value etc..
//
//  2. Run the example with the following args
//       dwi.nhdr 80 Tensors.mhd FractionalAnisotropy.mhd
RelativeAnisotropy.mhd 1
//
//  3. You should find 30 gradient images, 1 reference image, the FA and RA
images
//     in your working directory, which you can fire up in your favourite
volume
//     browser.

The reconstructed images shoudl match what's uploaded at :
  http://public.kitware.com/pub/itk/Data/DTI/Reconstructed/


Are you saying that if you run this example on this data, you do not get the
output uploaded above ?



thanks for your help,
>
>
>
>
>
> ------------------------------
> From: albagarin1986 at hotmail.com
> To: vincent-magnotta at uiowa.edu; insight-users at itk.org
> Date: Thu, 17 Feb 2011 08:16:27 +0000
>
> Subject: Re: [Insight-users] DiffusionTensor3DReconstructionFilter
>
> Thanks, i am taking a look to it at the moment.
>
>
>
>
>
>
> ------------------------------
> From: vincent-magnotta at uiowa.edu
> To: albagarin1986 at hotmail.com; insight-users at itk.org
> Subject: Re: [Insight-users] DiffusionTensor3DReconstructionFilter
> Date: Wed, 16 Feb 2011 18:27:25 +0000
>
>  Here is a link to a program that we write that uses the filter. We use
> NRRD files as input to this program.
>
>
> http://www.nitrc.org/plugins/scmsvn/viewcvs.php/GTRACT/Cmdline/gtractTensor.cxx?root=vmagnotta&view=markup
>
>  Vince
>
>   --
> Associate Professor
> Department of Radiology
> 0453-D JCP
> 200 Hawkins Drive
> Iowa City, IA 52242
> E-mail: vincent-magnotta at uiowa.edu
> Phone: 319-356-8255 Fax: 319-353-6275
> Website: http://www.healthcare.uiowa.edu/Radiology
>
>   From: alba garin <albagarin1986 at hotmail.com>
> Date: Wed, 16 Feb 2011 08:15:47 +0000
> To: <insight-users at itk.org>
> Subject: [Insight-users] DiffusionTensor3DReconstructionFilter
>
>  Hi everyone,
>
>  im getting mad trying to use the DiffusionTensor3DReconstructionFilter
> with a nrrd diffusion file. I store properly the gradients and after using
> the filter I get a image with pixels of DiffusionTensor3D. the problem is
> that this image has as voxels only zeros...
> anyone can help me, please?
>
>  Thanks,
> Alba
>
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