[Insight-users] DiffusionTensor3DReconstructionFilter

Mon Feb 21 09:44:06 EST 2011

Hi again,
I got the reason of my problem thanks to a partner of my job. The problem was that i did not restrict the area of the image so i was obtaining the tensor of a part of the image that was air, not brain so i was getting nothing. sorry for my ignorance. thanks, Alba

From: albagarin1986 at hotmail.com
To: karthik.krishnan at kitware.com
CC: vincent-magnotta at uiowa.edu; insight-users at itk.org
Subject: RE: [Insight-users] DiffusionTensor3DReconstructionFilter
Date: Mon, 21 Feb 2011 08:52:14 +0000

I get this output. But i need to use the tensor to get the eigenvalues and eigenvectors. So i modified the example to get those values and:- i used almost all the code from the example - it built with no errors. - i get the tensor image from the output of the filter. when obtaining the components of the tensor all of them are 0.000000 and when computing the eigenvalues and eigenvectors using the methods from DiffusionTensor3D.ComputeEigenAnalysis i get that all the eigenvalues are 0.0000000 - the only thing i get is that the eigenvectors(0,0) is 1.0000000000000 and eigenvectors(0,1) and eigenvectors(0,2) for example are 0.0000000000000
i checked all the examples you posted me below (thanks, by the way).

Date: Mon, 21 Feb 2011 14:06:49 +0530
Subject: Re: [Insight-users] DiffusionTensor3DReconstructionFilter
From: karthik.krishnan at kitware.com
To: albagarin1986 at hotmail.com
CC: vincent-magnotta at uiowa.edu; insight-users at itk.org

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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Kitware offers ITK Training Courses, for more information visit:

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