nipype.interfaces.slicer.registration.brainsresample module

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BRAINSResample

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: 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.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

defaultValuea float

Default voxel value. Maps to a command-line argument: --defaultValue %f.

deformationVolumea pathlike object or string representing an existing file

Displacement Field to be used to warp the image. Maps to a command-line argument: --deformationVolume %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

gridSpacinga list of items which are an integer

Add warped grid to output image to help show the deformation that occurred 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 making a 2D image of grid lines from the 3D space . Maps to a command-line argument: --gridSpacing %s.

inputVolumea pathlike object or string representing an existing file

Image To Warp. Maps to a command-line argument: --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. Maps to a command-line argument: --interpolationMode %s.

inverseTransforma boolean

True/False is to compute inverse of given transformation. Default is false. Maps to a command-line argument: --inverseTransform.

numberOfThreadsan integer

Explicitly specify the maximum number of threads to use. Maps to a command-line argument: --numberOfThreads %d.

outputVolumea boolean or a pathlike object or string representing a file

Resulting deformed image. Maps to a command-line argument: --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. Maps to a command-line argument: --pixelType %s.

referenceVolumea pathlike object or string representing an existing file

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. Maps to a command-line argument: --referenceVolume %s.

warpTransforma pathlike object or string representing an existing file

Filename for the BRAINSFit transform used in place of the deformation field. Maps to a command-line argument: --warpTransform %s.

outputVolumea pathlike object or string representing an existing file

Resulting deformed image.