Modules:ResampleVolume2-Documentation

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Module Name

MyModule

Module with panels expanded

Original Image [1]

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 resample an image and already knows the transform to apply to it. Its principal advantages resides in the fact that one can apply any kind of transform supported by ITK (rigid, affine and non-rigid) and can choose between the most commonly used interpolators.
• The transform can be passed as an ITKTransform file using the command line, or directly as a transform in Slicer3. In the latter case, the transform can only be rigid or affine.
• It also allows changing the spacing, the orientation, the size or the origin of the image.

Quick Tour of Features and Use

• 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: It should normally not be modified when using this module directly in Slicer3. It specifies whether the matrix is expressed in LPS or RAS coordinate space. This option can also be set when using the module in command line if the given transform is in RAS coordinate space (respectively LPS) and the input volume is in LPS coordinate space (respectively RAS). Be careful: When passing manually the transform, the coordinate space modification is directly applied on the given transform. However, when passing the transform through a file or a transform node, it is the input volume coordinate space that is modified and the transform is left unchanged (so that any kind of transform supported by ITK is also supported by this module). If one sets the output volume parameters manually, one has to pay attention to the fact that in that case the given parameters are considered to be in the transform coordinate space!!!
• 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. This option can only be used if the transform is rigid or affine.
• 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 (only relevant if the selected interpolator is bs).
• Output Parameters: One can overwrite the reference volume parameters by setting manually the spacing, size, origin (as a fiducial), and direction matrix (also known as space directions).

Development

Dependencies

None

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

link to ResampleVolume2.

More Information

When Using the module in command line

• The Transform can be given through an ITK Transform file. An example of such files is visible below.

#Insight Transform File V1.0
# Transform 0
Transform: AffineTransform_double_3_3
Parameters: 1.73205080756880 0.5 0 -0.5 .8660254037844 0 0 0 1.5 15 32 27
FixedParameters: 40 35 20

• Be Careful : The transform file must have an empty line after the fixed parameters
• The Fixed Parameters are the coordinates of the center of rotation
• The Parameters are written in the same format as follows:
  • 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.
• A transform file can contain multiple transforms. The module will apply all of them.

Acknowledgment

Include funding and other support here.

References

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

[1] http://www.bic.mni.mcgill.ca/brainweb/