Documentation/4.2/Modules/ResampleDTIVolume

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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: Demian Wassermann, SPL, LMI, PNL, Brigham and Women's Hospital, Harvard Medical School
Contact: Demian Wassermann,
Contributor1: Raúl San José-Estepar
Contributor2: Lauren O'Donnel

Surgical Planning Laboratory  
NAC  

Module Description

Resampling an image is a very important task in image analysis. It is especially important in the frame of image registration. This module implements DT image resampling through the use of itk Transforms. The resampling is controlled by the Output Spacing. "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.


Use Cases

Most frequently used for these scenarios:

  • Use Case 1:
  • Use Case 2:

Tutorials

Links to tutorials that use this module

Panels and their use

Parameters:

  • Input/Ouput
    • Input Volume: Input volume to be resampled
    • Output Volume: Resampled Volume
    • Reference Volume (To Set Output Parameters): Reference Volume (spacing,size,orientation,origin)
  • Transform Parameters
    • Transform Node:
    • Deformation Field Volume: File containing the deformation field (3D vector image containing vectors with 3 components)
    • Displacement or h-Field: Set if the deformation field is an -Field
  • Processing Options
    • Interpolation: Sampling algorithm (linear , nn (nearest neighborhoor), ws (WindowedSinc), bs (BSpline) )
    • Tensors Correction: Correct the tensors if computed tensor is not semi-definite positive
  • Tensor Transform Type
    • Finite Strain (FS) or \nPreservation of the Principal Direction (PPD): Chooses between 2 methods to transform the tensors: Finite Strain (FS), faster but less accurate, or Preservation of the Principal Direction (PPD)
  • Advanced Transform Parameters
    • Transforms Order: Select in what order the transforms are read
    • Not a Bulk Transform: 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 Orientation between transform and image is different (RAS/LPS) (warning: if the transform is a Transform Node in Slicer3, do not select)
  • Advanced Rigid/Affine Parameters
    • Rotation Center: Center of rotation (only for rigid and affine transforms)
    • Centered Transform: Set the center of the transformation to the center of the input image (only for rigid and affine transforms)
    • Image Center: Image to use to center the transform (used only if "Centered Transform" is selected)
    • Inverse Transformation: Inverse the transformation before applying it from output image to input image (only for rigid and affine transforms)
  • Manual Output Parameters
    • Spacing: Spacing along each dimension (0 means use input spacing)
    • Size: Size along each dimension (0 means use input size)
    • Origin: Origin of the output Image
    • Direction Matrix: 9 parameters of the direction matrix by rows (ijk to LPS if LPS transform, ijk to RAS if RAS transform)
  • Advanced Resampling Parameters
    • Number Of Threads: Number of thread used to compute the output image
    • Default Pixel Value: Default pixel value for samples falling outside of the input region
  • Windowed Sinc Interpolate Function Parameters
    • Window Function: Window Function \nh = Hamming \nc = Cosine \nw = Welch \nl = Lanczos \nb = Blackman
  • BSpline Interpolate Function Parameters
    • Spline Order: Spline Order (Spline order may be from 0 to 5)
  • Manual Transform (Used only if no transform node set)
    • Transform Matrix: 12 parameters of the transform matrix by rows ( --last 3 being translation-- )
    • Transform Type: Transform algorithm\nrt = Rigid Transform\na = Affine Transform


Similar Modules

  • Point to other modules that have similar functionality

References

Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation

Information for Developers