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For the stable Slicer documentation, visit the 4.6 page.

Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Francois Budin, NIRAL
Contact: Ryan Eckbo,


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.

Warning: To resample DWMR Images, use nrrd input and output files.

Warning: Do not use to resample Diffusion Tensor Images, tensors would not be reoriented

Use Cases




Panels and their use


  • Input/Output: Input/output parameters
    • Input Volume (inputVolume): Input Volume to be resampled
    • Output Volume (outputVolume): Resampled Volume
    • Reference Volume (To Set Output Parameters) (referenceVolume): Reference Volume (spacing,size,orientation,origin)
  • Transform Parameters: Parameters used to transform the input image into the output image
    • Transform Node (transformationFile):
    • Deformation Field Volume (deffield): File containing the deformation field (3D vector image containing vectors with 3 components)
    • Displacement or H-Field (typeOfField): Set if the deformation field is an h-Field
  • Interpolation Type:
    • Interpolation (interpolationType): Sampling algorithm (linear or nn (nearest neighborhoor), ws (WindowedSinc), bs (BSpline) )
  • Advanced Transform Parameters: Those parameters should normally not be modified
    • Transforms Order (transformsOrder): Select in what order the transforms are read
    • Not a Bulk Transform (notbulk): The transform following the BSpline transform is not set as a bulk transform for the BSpline transform
    • Space Orientation inconsistency (between transform and image) (space): Space Orientation between transform and image is different (RAS/LPS) (warning: if the transform is a Transform Node in Slicer3, do not select)
  • Rigid/Affine Parameters:
    • Rotation Point (rotationPoint): Rotation Point in case of rotation around a point (otherwise useless)
    • Centered Transform (centeredTransform): Set the center of the transformation to the center of the input image
    • Image Center (imageCenter): Image to use to center the transform (used only if "Centered Transform" is selected)
    • Inverse ITK Transformation (inverseITKTransformation): Inverse the transformation before applying it from output image to input image
  • Manual Output Parameters: Parameters of the output image
    • Spacing (outputImageSpacing): Spacing along each dimension (0 means use input spacing)
    • Size (outputImageSize): Size along each dimension (0 means use input size)
    • Origin (outputImageOrigin): Origin of the output Image
    • Direction Matrix (directionMatrix): 9 parameters of the direction matrix by rows (ijk to LPS if LPS transform, ijk to RAS if RAS transform)
  • Advanced Resampling Parameters: Parameters used for resampling
    • Number Of Thread (numberOfThread): Number of thread used to compute the output image
    • Default Pixel Value (defaultPixelValue): Default pixel value for samples falling outside of the input region
  • Windowed Sinc Interpolate Function Parameters: Parameters used for the Windowed Sinc interpolation
    • Window Function (windowFunction): Window Function \nh = Hamming \nc = Cosine \nw = Welch \nl = Lanczos \nb = Blackman
  • BSpline Interpolate Function Parameters: Parameters used for the BSpline interpolation
    • Spline Order (splineOrder): Spline Order
  • Manual Transform (Only used if no transform node set):
    • Transform Matrix (transformMatrix): 12 parameters of the transform matrix by rows ( --last 3 being translation-- )
    • Transform (transformType): Transform algorithm\nrt = Rigid Transform\na = Affine Transform

List of parameters generated transforming this XML file using this XSL file. To update the URL of the XML file, edit this page.

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