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interfaces.slicer.registration.brainsresample

BRAINSResample

Link to code

Wraps command **/home/raid3/gorgolewski/software/slicer/Slicer –launch BRAINSResample **

title: Resample Image (BRAINS)

category: Registration

description:
This program resamples an image image using a deformation field or a transform (BSpline, Affine, Rigid, etc.).

version: 3.0.0

documentation-url: http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSResample

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson.

acknowledgements: The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.

Inputs:

[Mandatory]

[Optional]
args: (a string)
        Additional parameters to the command
defaultValue: (a float)
        Default voxel value
deformationVolume: (an existing file name)
        Displacement Field to be used to warp the image
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
gridSpacing: (an integer)
        Add warped grid to output image to help show the deformation that occured with specified
        spacing.   A spacing of 0 in a dimension indicates that grid lines should be rendered to
        fall exactly (i.e. do not allow displacements off that plane).  This is useful for
        makeing a 2D image of grid lines from the 3D space
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
inputVolume: (an existing file name)
        Image To Warp
interpolationMode: ('NearestNeighbor' or 'Linear' or 'ResampleInPlace' or 'BSpline' or
         'WindowedSinc' or 'Hamming' or 'Cosine' or 'Welch' or 'Lanczos' or 'Blackman')
        Type of interpolation to be used when applying transform to moving volume.  Options are
        Linear, ResampleInPlace, NearestNeighbor, BSpline, or WindowedSinc
inverseTransform: (a boolean)
        True/False is to compute inverse of given transformation. Default is false
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Resulting deformed image
pixelType: ('float' or 'short' or 'ushort' or 'int' or 'uint' or 'uchar' or 'binary')
        Specifies the pixel type for the input/output images.  The 'binary' pixel type uses a
        modified algorithm whereby the image is read in as unsigned char, a signed distance map
        is created, signed distance map is resampled, and then a thresholded image of type
        unsigned char is written to disk.
referenceVolume: (an existing file name)
        Reference image used only to define the output space. If not specified, the warping is
        done in the same space as the image to warp.
warpTransform: (an existing file name)
        Filename for the BRAINSFit transform used in place of the deformation field

Outputs:

outputVolume: (an existing file name)
        Resulting deformed image