[Insight-users] Re: [slicer-devel] Tractography flowchart : Diffusion Weigthed Image --> Tensor Images

[Luis Ibanez]

Hi Mohammad,

In case you don't have a way of computing Tensor images from your
Diffusion images, You can use the following ITK filter to do so:

         DiffusionTensor3DReconstructionImageFilter

http://www.itk.org/Insight/Doxygen/html/classitk_1_1DiffusionTensor3DReconstructionImageFilter.html



   Regards,


       Luis


-------------------
Raul San Jose wrote:
> Hi Mohammad,
> 
> The core class taking care of the tractography is
> vtkTensorUtil/src/vtkHyperStreamlineDTMRI.cxx
> 
> Assuming that you have a way of computing tensors from your diffusion 
> weighted images, you can use the previous class to compute streamlines, 
> i.e. tracts. You could directly use this result in your own application 
> and renderer the fibers by creating a mapper and actor.
> 
> The Slicer does not directly use vtkHyperStremalineDTMRI but it's used in
> vtkDTMRI/cxx/vtkSeedTracts.cxx
> 
> The way the seeding and displaying of tracts in the Slicer works is as 
> follows:
> 
> vtkDTMRI/cxx/ vtkMultipleStreamlineController.cxx is a handler class 
> that takes care of coordinating the efforts of seeding, displaying and 
> saving tracts from a given tensor volume (vtkImageData).The seeding, 
> i.e. creation of tracts, is delegated to vtkSeedTracts. The result of 
> calling this class is a collection of "Streamlines". For displaying, 
> vtkDisplayTracts is used. vtkDisplayTracts takes a collection of 
> "Streamlines", i.e. tracts", and a given vtk renderer and takes care of 
> creating the proper graphic objects to display the tracts in the 
> rendererer. vtkDisplayTracts also offers an interface to delete a given 
> tract or even delete a tract that has been picked by the user.
> 
> You might want to use this architecture in your own application for 
> seeding and displaying tracts if you don't mind the extra complexity 
> that brings.
> 
> I hope this is helpful
> 
> /Raul
> 
> 
> Mohammad Nazemzadeh wrote:
> 
>> Dear All,
>>  
>> I want to implement an application for Tractography that extract and 
>> display Tracts using Diffusion images. I have implemented some filters 
>> in ITK for writing FA, RA, RGB, etc. and now I want to use 3D Slicer 
>> modules (vtkDTMRI and vtkTensorUtil) for complete my work. I have 
>> downloaded source Cxx codes of these classes but lack of documentation 
>> of these modules caused that I can't find the work flow for using 
>> these classes for display fibres tracts. I guess the first step is 
>> using vtkImageDiffusionTensor class to extract tensors from diffusion 
>> images but other steps are not clear to me.
>> Any help will be appreciated.
>>  
>> Thank you in advance,
>>