interfaces.slicer.filtering.resamplescalarvectordwivolume¶
ResampleScalarVectorDWIVolume¶
Wraps the executable command ``ResampleScalarVectorDWIVolume ``.
title: Resample Scalar/Vector/DWI Volume
category: Filtering
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
version: 0.1
documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleScalarVectorDWIVolume
contributor: Francois Budin (UNC)
acknowledgements: 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 http://nihroadmap.nih.gov/bioinformatics
Inputs:
[Optional]
origin: (a list of items which are any value)
Origin of the output Image
argument: ``--origin %s``
defField: (an existing file name)
File containing the deformation field (3D vector image containing
vectors with 3 components)
argument: ``--defField %s``
window_function: ('h' or 'c' or 'w' or 'l' or 'b')
Window Function , h = Hamming , c = Cosine , w = Welch , l = Lanczos
, b = Blackman
argument: ``--window_function %s``
image_center: ('input' or 'output')
Image to use to center the transform (used only if 'Centered
Transform' is selected)
argument: ``--image_center %s``
size: (a list of items which are a float)
Size along each dimension (0 means use input size)
argument: ``--size %s``
spline_order: (an integer (int or long))
Spline Order
argument: ``--spline_order %d``
transform: ('rt' or 'a')
Transform algorithm, rt = Rigid Transform, a = Affine Transform
argument: ``--transform %s``
centered_transform: (a boolean)
Set the center of the transformation to the center of the input
image
argument: ``--centered_transform ``
transform_order: ('input-to-output' or 'output-to-input')
Select in what order the transforms are read
argument: ``--transform_order %s``
Inverse_ITK_Transformation: (a boolean)
Inverse the transformation before applying it from output image to
input image
argument: ``--Inverse_ITK_Transformation ``
direction_matrix: (a list of items which are a float)
9 parameters of the direction matrix by rows (ijk to LPS if LPS
transform, ijk to RAS if RAS transform)
argument: ``--direction_matrix %s``
interpolation: ('linear' or 'nn' or 'ws' or 'bs')
Sampling algorithm (linear or nn (nearest neighborhoor), ws
(WindowedSinc), bs (BSpline) )
argument: ``--interpolation %s``
outputVolume: (a boolean or a file name)
Resampled Volume
argument: ``%s``, position: -1
number_of_thread: (an integer (int or long))
Number of thread used to compute the output image
argument: ``--number_of_thread %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
spacing: (a list of items which are a float)
Spacing along each dimension (0 means use input spacing)
argument: ``--spacing %s``
hfieldtype: ('displacement' or 'h-Field')
Set if the deformation field is an h-Field
argument: ``--hfieldtype %s``
rotation_point: (a list of items which are any value)
Rotation Point in case of rotation around a point (otherwise
useless)
argument: ``--rotation_point %s``
notbulk: (a boolean)
The transform following the BSpline transform is not set as a bulk
transform for the BSpline transform
argument: ``--notbulk ``
default_pixel_value: (a float)
Default pixel value for samples falling outside of the input region
argument: ``--default_pixel_value %f``
transform_matrix: (a list of items which are a float)
12 parameters of the transform matrix by rows ( --last 3 being
translation-- )
argument: ``--transform_matrix %s``
Reference: (an existing file name)
Reference Volume (spacing,size,orientation,origin)
argument: ``--Reference %s``
transformationFile: (an existing file name)
argument: ``--transformationFile %s``
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
inputVolume: (an existing file name)
Input Volume to be resampled
argument: ``%s``, position: -2
spaceChange: (a boolean)
Space Orientation between transform and image is different (RAS/LPS)
(warning: if the transform is a Transform Node in Slicer3, do not
select)
argument: ``--spaceChange ``
Outputs:
outputVolume: (an existing file name)
Resampled Volume