interfaces.slicer.filtering.resamplescalarvectordwivolume

ResampleScalarVectorDWIVolume

Link to code

Wraps 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:

[Mandatory]

[Optional]
Inverse_ITK_Transformation: (a boolean)
        Inverse the transformation before applying it from output image to
        input image
        flag: --Inverse_ITK_Transformation
Reference: (an existing file name)
        Reference Volume (spacing,size,orientation,origin)
        flag: --Reference %s
args: (a unicode string)
        Additional parameters to the command
        flag: %s
centered_transform: (a boolean)
        Set the center of the transformation to the center of the input
        image
        flag: --centered_transform
defField: (an existing file name)
        File containing the deformation field (3D vector image containing
        vectors with 3 components)
        flag: --defField %s
default_pixel_value: (a float)
        Default pixel value for samples falling outside of the input region
        flag: --default_pixel_value %f
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)
        flag: --direction_matrix %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
hfieldtype: ('displacement' or 'h-Field')
        Set if the deformation field is an h-Field
        flag: --hfieldtype %s
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
image_center: ('input' or 'output')
        Image to use to center the transform (used only if 'Centered
        Transform' is selected)
        flag: --image_center %s
inputVolume: (an existing file name)
        Input Volume to be resampled
        flag: %s, position: -2
interpolation: ('linear' or 'nn' or 'ws' or 'bs')
        Sampling algorithm (linear or nn (nearest neighborhoor), ws
        (WindowedSinc), bs (BSpline) )
        flag: --interpolation %s
notbulk: (a boolean)
        The transform following the BSpline transform is not set as a bulk
        transform for the BSpline transform
        flag: --notbulk
number_of_thread: (an integer (int or long))
        Number of thread used to compute the output image
        flag: --number_of_thread %d
origin: (a list of items which are any value)
        Origin of the output Image
        flag: --origin %s
outputVolume: (a boolean or a file name)
        Resampled Volume
        flag: %s, position: -1
rotation_point: (a list of items which are any value)
        Rotation Point in case of rotation around a point (otherwise
        useless)
        flag: --rotation_point %s
size: (a list of items which are a float)
        Size along each dimension (0 means use input size)
        flag: --size %s
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)
        flag: --spaceChange
spacing: (a list of items which are a float)
        Spacing along each dimension (0 means use input spacing)
        flag: --spacing %s
spline_order: (an integer (int or long))
        Spline Order
        flag: --spline_order %d
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
transform: ('rt' or 'a')
        Transform algorithm, rt = Rigid Transform, a = Affine Transform
        flag: --transform %s
transform_matrix: (a list of items which are a float)
        12 parameters of the transform matrix by rows ( --last 3 being
        translation-- )
        flag: --transform_matrix %s
transform_order: ('input-to-output' or 'output-to-input')
        Select in what order the transforms are read
        flag: --transform_order %s
transformationFile: (an existing file name)
        flag: --transformationFile %s
window_function: ('h' or 'c' or 'w' or 'l' or 'b')
        Window Function , h = Hamming , c = Cosine , w = Welch , l = Lanczos
        , b = Blackman
        flag: --window_function %s

Outputs:

outputVolume: (an existing file name)
        Resampled Volume