Difference between revisions of "2008 Winter Project Week:Resampling DTIs with Slicer3"

From NAMIC Wiki
Jump to: navigation, search
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
{|
 
{|
 
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
 
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
 +
|[[Image:Original_tensor_ellipsoid.png|thumb|320px |Tensor Phantom ]]
 +
|[[Image:scaled_tensor_ellipsoid.png|thumb|320px |Tensor Phantom after scaling transformation]]
 
|}
 
|}
  
Line 13: Line 15:
  
 
<h1>Objective</h1>
 
<h1>Objective</h1>
The goal of this project is to develop a command line module for slicer 3 to resample DT images. This module will be compatible with several ITK 3D transforms (rigid, affine and non-rigid) and implements different diffusion tensor interpolations.
+
The goal of this project is to develop a command line module for slicer 3 to resample DT images. This module is compatible with several ITK 3D transforms (rigid, affine and non-rigid). These transforms can be pass as an ITKTransformFile using the command line, or directly as a transform in Slicer3. It also allows change the spacing, the orientation, the size or the origin of the image. This module implements different diffusion tensor interpolations and the structure of the program makes it easy to add new interpolations or new transformations.
  
 
</div>
 
</div>
Line 20: Line 22:
  
 
<h1>Approach, Plan </h1>
 
<h1>Approach, Plan </h1>
Our approach is to build the ITK infrastructure (ITK diffusion tensor interpolators and ITK diffusion tensor transforms) to support this module. Our main purpose at the Project Week is to implement a non-rigid transform for diffusion tensor images.
+
Our approach is to build the ITK infrastructure (ITK diffusion tensor interpolators and ITK diffusion tensor transforms) to support this module. Our main purpose at the Project Week is to implement a non-rigid transform for diffusion tensor images.
 
</div>
 
</div>
  
Line 27: Line 29:
 
<h1>Progress</h1>
 
<h1>Progress</h1>
  
The module currently supports:
+
====Jan 2008 Project Week====
*Several blockwise diffusion tensor interpolations
+
 
**Nearest Neighborhood
+
The project week allowed to integrate the module into Slicer3. It is now available in Slicer3 TransformIO branch. The support of the non-rigid transforms has been added. The list of the currently supported transforms is the following:
**Linear
+
*Rigid3D
**BSpline
+
*Affine - Finite Strain
*Some Transforms
+
*Affine - Preservation of Principal Direction
**Rigid3D
+
*Non-rigid transforms (not tested yet)
**Affine - Finite Strain
+
 
**Affine - Preservation of Principal Direction
+
Several blockwise diffusion tensor interpolations are also available:
To implement:
+
*Nearest Neighborhood
*non-rigid transforms
+
*Linear
*better interpolations
+
*BSpline
 +
*Windowed Sinc
 +
 
 +
The next step is to implement new interpolations (ie separating the shape and the orientation of the tensors).
 +
 
 
</div>
 
</div>
  
Line 44: Line 50:
  
 
</div>
 
</div>
 
  
 
===References===
 
===References===
 
* D.C. Alexander, C. Pierpaoli, P.J. Basser, J.C. Gee. Spatial Transformations of Diffusion Tensor Magnetic Resonance Images, IEEE Transactions on medical imaging, vol. 20, No. 11, November 2001
 
* D.C. Alexander, C. Pierpaoli, P.J. Basser, J.C. Gee. Spatial Transformations of Diffusion Tensor Magnetic Resonance Images, IEEE Transactions on medical imaging, vol. 20, No. 11, November 2001

Latest revision as of 22:21, 14 February 2008

Home < 2008 Winter Project Week:Resampling DTIs with Slicer3
Tensor Phantom
Tensor Phantom after scaling transformation


Key Investigators

  • BWH: Francois Budin, Sylvain Bouix
  • GE: Xiaodong Tao

Objective

The goal of this project is to develop a command line module for slicer 3 to resample DT images. This module is compatible with several ITK 3D transforms (rigid, affine and non-rigid). These transforms can be pass as an ITKTransformFile using the command line, or directly as a transform in Slicer3. It also allows change the spacing, the orientation, the size or the origin of the image. This module implements different diffusion tensor interpolations and the structure of the program makes it easy to add new interpolations or new transformations.

Approach, Plan

Our approach is to build the ITK infrastructure (ITK diffusion tensor interpolators and ITK diffusion tensor transforms) to support this module. Our main purpose at the Project Week is to implement a non-rigid transform for diffusion tensor images.

Progress

Jan 2008 Project Week

The project week allowed to integrate the module into Slicer3. It is now available in Slicer3 TransformIO branch. The support of the non-rigid transforms has been added. The list of the currently supported transforms is the following:

  • Rigid3D
  • Affine - Finite Strain
  • Affine - Preservation of Principal Direction
  • Non-rigid transforms (not tested yet)

Several blockwise diffusion tensor interpolations are also available:

  • Nearest Neighborhood
  • Linear
  • BSpline
  • Windowed Sinc

The next step is to implement new interpolations (ie separating the shape and the orientation of the tensors).


References

  • D.C. Alexander, C. Pierpaoli, P.J. Basser, J.C. Gee. Spatial Transformations of Diffusion Tensor Magnetic Resonance Images, IEEE Transactions on medical imaging, vol. 20, No. 11, November 2001