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# interfaces.semtools.registration.brainsresample

## BRAINSResample

Link to code

Wraps command ** BRAINSResample **

title: Resample Image (BRAINS)

category: Registration

description: This program collects together three common image processing tasks that all involve resampling an image volume: Resampling to a new resolution and spacing, applying a transformation (using an ITK transform IO mechanisms) and Warping (using a vector image deformation field). Full documentation available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample.

version: 3.0.0

documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/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 (ITKv3 or earlier)
            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 (ITKv3 or earlier) or composite
            transform file (ITKv4)
            flag: --warpTransform %s

Outputs:

    outputVolume: (an existing file name)
            Resulting deformed image