interfaces.slicer.registration.brainsresample

BRAINSResample

Link to code

Wraps command **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 unicode string)
        Additional parameters to the command
        flag: %s
defaultValue: (a float)
        Default voxel value
        flag: --defaultValue %f
deformationVolume: (an existing file name)
        Displacement Field to be used to warp the image
        flag: --deformationVolume %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
gridSpacing: (a list of items which are an integer (int or long))
        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
        flag: --gridSpacing %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
inputVolume: (an existing file name)
        Image To Warp
        flag: --inputVolume %s
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
        flag: --interpolationMode %s
inverseTransform: (a boolean)
        True/False is to compute inverse of given transformation. Default is
        false
        flag: --inverseTransform
numberOfThreads: (an integer (int or long))
        Explicitly specify the maximum number of threads to use.
        flag: --numberOfThreads %d
outputVolume: (a boolean or a file name)
        Resulting deformed image
        flag: --outputVolume %s
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.
        flag: --pixelType %s
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.
        flag: --referenceVolume %s
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
warpTransform: (an existing file name)
        Filename for the BRAINSFit transform used in place of the
        deformation field
        flag: --warpTransform %s

Outputs:

outputVolume: (an existing file name)
        Resulting deformed image