nipype.interfaces.semtools.registration.brainsresample module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
BRAINSResample¶
Bases: SEMLikeCommandLine
Wrapped executable:
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.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.defaultValue (a float) – Default voxel value. Maps to a command-line argument:
--defaultValue %f.deformationVolume (a pathlike object or string representing an existing file) – Displacement Field to be used to warp the image (ITKv3 or earlier). Maps to a command-line argument:
--deformationVolume %s.environ (a 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:
{})gridSpacing (a 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.inputVolume (a 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.inverseTransform (a boolean) – True/False is to compute inverse of given transformation. Default is false. Maps to a command-line argument:
--inverseTransform.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a 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.referenceVolume (a 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.warpTransform (a pathlike object or string representing an existing file) – Filename for the BRAINSFit transform (ITKv3 or earlier) or composite transform file (ITKv4). Maps to a command-line argument:
--warpTransform %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Resulting deformed image.