Modules:ResampleVolume2-Documentation

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Module Name

MyModule

Module with panels expanded

Original Image

Transformed Image

General Information

Module Type & Category

Type: CLI

Category: Filtering

Authors, Collaborators & Contact

• Francois Budin
• Sylvain Bouix, PNL
• Contact: Francois Budin , budin[at]bwh[dot]harvard[dot]edu

Module Description

This module implements image and vector-image resampling through the use of itk Transforms.It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

Usage

Examples, Use Cases & Tutorials

• This module is especially appropriate when one needs to transform an image and already knows the transformation to apply.

Quick Tour of Features and Use

List all the panels in your interface, their features, what they mean, and how to use them. For instance:

• Input/Output: Defines input and output files.
  • Input volume is the volume to resample,
  • Reference Volume (optional) is the volume used to set the sampling parameters (origin, spacing, orientation and dimensions). If it is not set, the input volume will be taken for reference.
  • Output volume is the name of the output.
• Resampling Parameters: Sets the number of threads used to perform the resampling.
• Transform Parameters: if the transform to be applied is in the slicer mrml tree, one can select it here.
• Manual Transform: if no tranform is set in previous panel, one can enter his own transform
  • Transform Matrix: a 12 parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix in column-major order (where the column index varies the fastest), the last 3 are a translation.
  • Transform: forces the transform to be of rigid or affine type (affine is default)
  • Space: specifies whether the matrix is expressed in LPS or RAS coordinate space. This option can also be set when using the module in commandline if the given transform is in RAS coordinate space (respectively LPS) and the input volume is in LPS coordinate space (respectively RAS).
• Rigid/Affine Parameters:
  • Rotation Point: uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.
  • Centered Transform: sets the center of the transformation to the center of the image.
  • Inverse ITK Transformation: inverses the transformation before applying it to the image
• Interpolation Type: sets the type of interpolation kernel to either linear, nearest neighbor (nn), windowed sinc (ws), or b-spline (bs).
• Windowed Sinc Interpolate Function Parameters: selects the type window function for the sinc interpolation h=hamming, c=cosine, w=welch, l=lanczos, b=blackman. This is only relevant if one selects ws as the interpolation type.
• BSpline Interpolate Function Parameters: The spline order.
• Output Parameters: if no reference volume is given, one can set the spacing, size, origin (as a fiducial), and direction matrix (also known as space directions) manually.

Development

Dependencies

Other modules or packages that are required for this module's use.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

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Links to documentation generated by doxygen.

More Information

Acknowledgment

Include funding and other support here.

References

Publications related to this module go here. Links to pdfs would be useful.