Resample DTI Volume


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.

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 -Field

Processing Options:

  • Interpolation (interpolationType): Sampling algorithm (linear , nn (nearest neighbor), ws (WindowedSinc), bs (BSpline) )

  • No Measurement Frame (noMeasurementFrame): Do not use the measurement frame that is in the input image to transform the tensors. Uses the image orientation instead

  • Tensors Correction (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) (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: 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)

Advanced Rigid/Affine Parameters:

  • Rotation Center (rotationPoint): Center of rotation (only for rigid and affine transforms)

  • Centered Transform (centeredTransform): Set the center of the transformation to the center of the input image (only for rigid and affine transforms)

  • Image Center (imageCenter): Image to use to center the transform (used only if “Centered Transform” is selected)

  • Inverse Transformation (inverseITKTransformation): Inverse the transformation before applying it from output image to input image (only for rigid and affine transforms)

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 Threads (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 (Spline order may be from 0 to 5)

Manual Transform (Used only if no transform node set):

  • Transform Matrix (transformMatrix): 12 parameters of the transform matrix by rows ( –last 3 being translation– )

  • Transform Type (transformType): Transform algorithm\nrt = Rigid Transform\na = Affine Transform


Francois Budin (UNC)


This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from