Home · Quickstart · User Guide and Examples · Interfaces Index · Developers · About · Nipy

# nipype.interfaces.slicer.registration.specialized module

Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.

## ACPCTransform

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `ACPCTransform`.

> title: ACPC Transform

> category: Registration.Specialized

> description: <p>Calculate a transformation from two lists of fiducial points.</p><p>ACPC line is two fiducial points, one at the anterior commissure and one at the posterior commissure. The resulting transform will bring the line connecting them to horizontal to the AP axis.</p><p>The midline is a series of points defining the division between the hemispheres of the brain (the mid sagittal plane). The resulting transform will put the output volume with the mid sagittal plane lined up with the AS plane.</p><p>Use the Filtering module<b>Resample Scalar/Vector/DWI Volume</b>to apply the transformation to a volume.</p>

> version: 1.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ACPCTransform

> license: slicer3

> contributor: Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)

> acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

> acpca list of items which are a list of from 3 to 3 items which are a float

>   ACPC line, two fiducial points, one at the anterior commissure and one at the posterior commissure. Maps to a command-line argument: `--acpc %s...`.

> argsa unicode string

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

> debugSwitcha boolean

>   Click if wish to see debugging output. Maps to a command-line argument: `--debugSwitch`.

> 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: `{}`)

> midlinea list of items which are a list of from 3 to 3 items which are a float

>   The midline is a series of points defining the division between the hemispheres of the brain (the mid sagittal plane). Maps to a command-line argument: `--midline %s...`.

> outputTransforma boolean or a pathlike object or string representing a file

>   A transform filled in from the ACPC and Midline registration calculation. Maps to a command-line argument: `--outputTransform %s`.

> outputTransforma pathlike object or string representing an existing file

>   A transform filled in from the ACPC and Midline registration calculation.

## BRAINSDemonWarp

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSDemonWarp`.

> title: Demon Registration (BRAINS)

> category: Registration.Specialized

> description:

>   This program finds a deformation field to warp a moving image onto a fixed image. The images must be of the same signal kind, and contain an image of the same kind of object. This program uses the Thirion Demons warp software in ITK, the Insight Toolkit. Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp.

> version: 3.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSDemonWarp

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

> contributor: This tool was developed by Hans J. Johnson and Greg Harris.

> 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 unicode string

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

> arrayOfPyramidLevelIterationsa list of items which are an integer (int or long)

>   The number of iterations for each pyramid level. Maps to a command-line argument: `--arrayOfPyramidLevelIterations %s`.

> backgroundFillValuean integer (int or long)

>   Replacement value to overwrite background when performing BOBF. Maps to a command-line argument: `--backgroundFillValue %d`.

> checkerboardPatternSubdivisionsa list of items which are an integer (int or long)

>   Number of Checkerboard subdivisions in all 3 directions. Maps to a command-line argument: `--checkerboardPatternSubdivisions %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: `{}`)

> fixedBinaryVolumea pathlike object or string representing an existing file

>   Mask filename for desired region of interest in the Fixed image. Maps to a command-line argument: `--fixedBinaryVolume %s`.

> fixedVolumea pathlike object or string representing an existing file

>   Required: input fixed (target) image. Maps to a command-line argument: `--fixedVolume %s`.

> gradient_type‘0’ or ‘1’ or ‘2’

>   Type of gradient used for computing the demons force (0 is symmetrized, 1 is fixed image, 2 is moving image). Maps to a command-line argument: `--gradient_type %s`.

> guia boolean

>   Display intermediate image volumes for debugging. Maps to a command-line argument: `--gui`.

> histogramMatcha boolean

>   Histogram Match the input images. This is suitable for images of the same modality that may have different absolute scales, but the same overall intensity profile. Maps to a command-line argument: `--histogramMatch`.

> initializeWithDisplacementFielda pathlike object or string representing an existing file

>   Initial deformation field vector image file name. Maps to a command-line argument: `--initializeWithDisplacementField %s`.

> initializeWithTransforma pathlike object or string representing an existing file

>   Initial Transform filename. Maps to a command-line argument: `--initializeWithTransform %s`.

> inputPixelType‘float’ or ‘short’ or ‘ushort’ or ‘int’ or ‘uchar’

>   Input volumes will be typecast to this format: float|short|ushort|int|uchar. Maps to a command-line argument: `--inputPixelType %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`.

> lowerThresholdForBOBFan integer (int or long)

>   Lower threshold for performing BOBF. Maps to a command-line argument: `--lowerThresholdForBOBF %d`.

> maskProcessingMode‘NOMASK’ or ‘ROIAUTO’ or ‘ROI’ or ‘BOBF’

>   What mode to use for using the masks: NOMASK|ROIAUTO|ROI|BOBF. If ROIAUTO is choosen, then the mask is implicitly defined using a otsu forground and hole filling algorithm. Where the Region Of Interest mode uses the masks to define what parts of the image should be used for computing the deformation field. Brain Only Background Fill uses the masks to pre-process the input images by clipping and filling in the background with a predefined value. Maps to a command-line argument: `--maskProcessingMode %s`.

> max_step_lengtha float

>   Maximum length of an update vector (0: no restriction). Maps to a command-line argument: `--max_step_length %f`.

> medianFilterSizea list of items which are an integer (int or long)

>   Median filter radius in all 3 directions. When images have a lot of salt and pepper noise, this step can improve the registration. Maps to a command-line argument: `--medianFilterSize %s`.

> minimumFixedPyramida list of items which are an integer (int or long)

>   The shrink factor for the first level of the fixed image pyramid. (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally full scale). Maps to a command-line argument: `--minimumFixedPyramid %s`.

> minimumMovingPyramida list of items which are an integer (int or long)

>   The shrink factor for the first level of the moving image pyramid. (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally full scale). Maps to a command-line argument: `--minimumMovingPyramid %s`.

> movingBinaryVolumea pathlike object or string representing an existing file

>   Mask filename for desired region of interest in the Moving image. Maps to a command-line argument: `--movingBinaryVolume %s`.

> movingVolumea pathlike object or string representing an existing file

>   Required: input moving image. Maps to a command-line argument: `--movingVolume %s`.

> neighborhoodForBOBFa list of items which are an integer (int or long)

>   Neighborhood in all 3 directions to be included when performing BOBF. Maps to a command-line argument: `--neighborhoodForBOBF %s`.

> numberOfBCHApproximationTermsan integer (int or long)

>   Number of terms in the BCH expansion. Maps to a command-line argument: `--numberOfBCHApproximationTerms %d`.

> numberOfHistogramBinsan integer (int or long)

>   The number of histogram levels. Maps to a command-line argument: `--numberOfHistogramBins %d`.

> numberOfMatchPointsan integer (int or long)

>   The number of match points for histrogramMatch. Maps to a command-line argument: `--numberOfMatchPoints %d`.

> numberOfPyramidLevelsan integer (int or long)

>   Number of image pyramid levels to use in the multi-resolution registration. Maps to a command-line argument: `--numberOfPyramidLevels %d`.

> numberOfThreadsan integer (int or long)

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

> outputCheckerboardVolumea boolean or a pathlike object or string representing a file

>   Genete a checkerboard image volume between the fixedVolume and the deformed movingVolume. Maps to a command-line argument: `--outputCheckerboardVolume %s`.

> outputDebuga boolean

>   Flag to write debugging images after each step. Maps to a command-line argument: `--outputDebug`.

> outputDisplacementFieldPrefixa unicode string

>   Displacement field filename prefix for writing separate x, y, and z component images. Maps to a command-line argument: `--outputDisplacementFieldPrefix %s`.

> outputDisplacementFieldVolumea boolean or a pathlike object or string representing a file

>   Output deformation field vector image (will have the same physical space as the fixedVolume). Maps to a command-line argument: `--outputDisplacementFieldVolume %s`.

> outputNormalizeda boolean

>   Flag to warp and write the normalized images to output. In normalized images the image values are fit-scaled to be between 0 and the maximum storage type value. Maps to a command-line argument: `--outputNormalized`.

> outputPixelType‘float’ or ‘short’ or ‘ushort’ or ‘int’ or ‘uchar’

>   OutputVolume will be typecast to this format: float|short|ushort|int|uchar. Maps to a command-line argument: `--outputPixelType %s`.

> outputVolumea boolean or a pathlike object or string representing a file

>   Required: output resampled moving image (will have the same physical space as the fixedVolume). Maps to a command-line argument: `--outputVolume %s`.

> promptUsera boolean

>   Prompt the user to hit enter each time an image is sent to the DebugImageViewer. Maps to a command-line argument: `--promptUser`.

> registrationFilterType‘Demons’ or ‘FastSymmetricForces’ or ‘Diffeomorphic’

>   Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic. Maps to a command-line argument: `--registrationFilterType %s`.

> seedForBOBFa list of items which are an integer (int or long)

>   Coordinates in all 3 directions for Seed when performing BOBF. Maps to a command-line argument: `--seedForBOBF %s`.

> smoothDisplacementFieldSigmaa float

>   A gaussian smoothing value to be applied to the deformation feild at each iteration. Maps to a command-line argument: `--smoothDisplacementFieldSigma %f`.

> upFieldSmoothinga float

>   Smoothing sigma for the update field at each iteration. Maps to a command-line argument: `--upFieldSmoothing %f`.

> upperThresholdForBOBFan integer (int or long)

>   Upper threshold for performing BOBF. Maps to a command-line argument: `--upperThresholdForBOBF %d`.

> use_vanilla_dema boolean

>   Run vanilla demons algorithm. Maps to a command-line argument: `--use_vanilla_dem`.

> outputCheckerboardVolumea pathlike object or string representing an existing file

>   Genete a checkerboard image volume between the fixedVolume and the deformed movingVolume.

> outputDisplacementFieldVolumea pathlike object or string representing an existing file

>   Output deformation field vector image (will have the same physical space as the fixedVolume).

> outputVolumea pathlike object or string representing an existing file

>   Required: output resampled moving image (will have the same physical space as the fixedVolume).

## FiducialRegistration

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `FiducialRegistration`.

> title: Fiducial Registration

> category: Registration.Specialized

> description: Computes a rigid, similarity or affine transform from a matched list of fiducials

> version: 0.1.0.$Revision$

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/TransformFromFiducials

> contributor: Casey B Goodlett (Kitware), Dominik Meier (SPL, BWH)

> acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%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: `{}`)

> fixedLandmarksa list of items which are a list of from 3 to 3 items which are a float

>   Ordered list of landmarks in the fixed image. Maps to a command-line argument: `--fixedLandmarks %s...`.

> movingLandmarksa list of items which are a list of from 3 to 3 items which are a float

>   Ordered list of landmarks in the moving image. Maps to a command-line argument: `--movingLandmarks %s...`.

> outputMessagea unicode string

>   Provides more information on the output. Maps to a command-line argument: `--outputMessage %s`.

> rmsa float

>   Display RMS Error. Maps to a command-line argument: `--rms %f`.

> saveTransforma boolean or a pathlike object or string representing a file

>   Save the transform that results from registration. Maps to a command-line argument: `--saveTransform %s`.

> transformType‘Translation’ or ‘Rigid’ or ‘Similarity’

>   Type of transform to produce. Maps to a command-line argument: `--transformType %s`.

> saveTransforma pathlike object or string representing an existing file

>   Save the transform that results from registration.

## VBRAINSDemonWarp

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `VBRAINSDemonWarp`.

> title: Vector Demon Registration (BRAINS)

> category: Registration.Specialized

> description:

>   This program finds a deformation field to warp a moving image onto a fixed image. The images must be of the same signal kind, and contain an image of the same kind of object. This program uses the Thirion Demons warp software in ITK, the Insight Toolkit. Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp.

> version: 3.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSDemonWarp

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

> contributor: This tool was developed by Hans J. Johnson and Greg Harris.

> 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 unicode string

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

> arrayOfPyramidLevelIterationsa list of items which are an integer (int or long)

>   The number of iterations for each pyramid level. Maps to a command-line argument: `--arrayOfPyramidLevelIterations %s`.

> backgroundFillValuean integer (int or long)

>   Replacement value to overwrite background when performing BOBF. Maps to a command-line argument: `--backgroundFillValue %d`.

> checkerboardPatternSubdivisionsa list of items which are an integer (int or long)

>   Number of Checkerboard subdivisions in all 3 directions. Maps to a command-line argument: `--checkerboardPatternSubdivisions %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: `{}`)

> fixedBinaryVolumea pathlike object or string representing an existing file

>   Mask filename for desired region of interest in the Fixed image. Maps to a command-line argument: `--fixedBinaryVolume %s`.

> fixedVolumea list of items which are a pathlike object or string representing an existing file

>   Required: input fixed (target) image. Maps to a command-line argument: `--fixedVolume %s...`.

> gradient_type‘0’ or ‘1’ or ‘2’

>   Type of gradient used for computing the demons force (0 is symmetrized, 1 is fixed image, 2 is moving image). Maps to a command-line argument: `--gradient_type %s`.

> guia boolean

>   Display intermediate image volumes for debugging. Maps to a command-line argument: `--gui`.

> histogramMatcha boolean

>   Histogram Match the input images. This is suitable for images of the same modality that may have different absolute scales, but the same overall intensity profile. Maps to a command-line argument: `--histogramMatch`.

> initializeWithDisplacementFielda pathlike object or string representing an existing file

>   Initial deformation field vector image file name. Maps to a command-line argument: `--initializeWithDisplacementField %s`.

> initializeWithTransforma pathlike object or string representing an existing file

>   Initial Transform filename. Maps to a command-line argument: `--initializeWithTransform %s`.

> inputPixelType‘float’ or ‘short’ or ‘ushort’ or ‘int’ or ‘uchar’

>   Input volumes will be typecast to this format: float|short|ushort|int|uchar. Maps to a command-line argument: `--inputPixelType %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`.

> lowerThresholdForBOBFan integer (int or long)

>   Lower threshold for performing BOBF. Maps to a command-line argument: `--lowerThresholdForBOBF %d`.

> makeBOBFa boolean

>   Flag to make Brain-Only Background-Filled versions of the input and target volumes. Maps to a command-line argument: `--makeBOBF`.

> max_step_lengtha float

>   Maximum length of an update vector (0: no restriction). Maps to a command-line argument: `--max_step_length %f`.

> medianFilterSizea list of items which are an integer (int or long)

>   Median filter radius in all 3 directions. When images have a lot of salt and pepper noise, this step can improve the registration. Maps to a command-line argument: `--medianFilterSize %s`.

> minimumFixedPyramida list of items which are an integer (int or long)

>   The shrink factor for the first level of the fixed image pyramid. (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally full scale). Maps to a command-line argument: `--minimumFixedPyramid %s`.

> minimumMovingPyramida list of items which are an integer (int or long)

>   The shrink factor for the first level of the moving image pyramid. (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally full scale). Maps to a command-line argument: `--minimumMovingPyramid %s`.

> movingBinaryVolumea pathlike object or string representing an existing file

>   Mask filename for desired region of interest in the Moving image. Maps to a command-line argument: `--movingBinaryVolume %s`.

> movingVolumea list of items which are a pathlike object or string representing an existing file

>   Required: input moving image. Maps to a command-line argument: `--movingVolume %s...`.

> neighborhoodForBOBFa list of items which are an integer (int or long)

>   Neighborhood in all 3 directions to be included when performing BOBF. Maps to a command-line argument: `--neighborhoodForBOBF %s`.

> numberOfBCHApproximationTermsan integer (int or long)

>   Number of terms in the BCH expansion. Maps to a command-line argument: `--numberOfBCHApproximationTerms %d`.

> numberOfHistogramBinsan integer (int or long)

>   The number of histogram levels. Maps to a command-line argument: `--numberOfHistogramBins %d`.

> numberOfMatchPointsan integer (int or long)

>   The number of match points for histrogramMatch. Maps to a command-line argument: `--numberOfMatchPoints %d`.

> numberOfPyramidLevelsan integer (int or long)

>   Number of image pyramid levels to use in the multi-resolution registration. Maps to a command-line argument: `--numberOfPyramidLevels %d`.

> numberOfThreadsan integer (int or long)

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

> outputCheckerboardVolumea boolean or a pathlike object or string representing a file

>   Genete a checkerboard image volume between the fixedVolume and the deformed movingVolume. Maps to a command-line argument: `--outputCheckerboardVolume %s`.

> outputDebuga boolean

>   Flag to write debugging images after each step. Maps to a command-line argument: `--outputDebug`.

> outputDisplacementFieldPrefixa unicode string

>   Displacement field filename prefix for writing separate x, y, and z component images. Maps to a command-line argument: `--outputDisplacementFieldPrefix %s`.

> outputDisplacementFieldVolumea boolean or a pathlike object or string representing a file

>   Output deformation field vector image (will have the same physical space as the fixedVolume). Maps to a command-line argument: `--outputDisplacementFieldVolume %s`.

> outputNormalizeda boolean

>   Flag to warp and write the normalized images to output. In normalized images the image values are fit-scaled to be between 0 and the maximum storage type value. Maps to a command-line argument: `--outputNormalized`.

> outputPixelType‘float’ or ‘short’ or ‘ushort’ or ‘int’ or ‘uchar’

>   OutputVolume will be typecast to this format: float|short|ushort|int|uchar. Maps to a command-line argument: `--outputPixelType %s`.

> outputVolumea boolean or a pathlike object or string representing a file

>   Required: output resampled moving image (will have the same physical space as the fixedVolume). Maps to a command-line argument: `--outputVolume %s`.

> promptUsera boolean

>   Prompt the user to hit enter each time an image is sent to the DebugImageViewer. Maps to a command-line argument: `--promptUser`.

> registrationFilterType‘Demons’ or ‘FastSymmetricForces’ or ‘Diffeomorphic’ or ‘LogDemons’ or ‘SymmetricLogDemons’

>   Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic|LogDemons|SymmetricLogDemons. Maps to a command-line argument: `--registrationFilterType %s`.

> seedForBOBFa list of items which are an integer (int or long)

>   Coordinates in all 3 directions for Seed when performing BOBF. Maps to a command-line argument: `--seedForBOBF %s`.

> smoothDisplacementFieldSigmaa float

>   A gaussian smoothing value to be applied to the deformation feild at each iteration. Maps to a command-line argument: `--smoothDisplacementFieldSigma %f`.

> upFieldSmoothinga float

>   Smoothing sigma for the update field at each iteration. Maps to a command-line argument: `--upFieldSmoothing %f`.

> upperThresholdForBOBFan integer (int or long)

>   Upper threshold for performing BOBF. Maps to a command-line argument: `--upperThresholdForBOBF %d`.

> use_vanilla_dema boolean

>   Run vanilla demons algorithm. Maps to a command-line argument: `--use_vanilla_dem`.

> weightFactorsa list of items which are a float

>   Weight fatctors for each input images. Maps to a command-line argument: `--weightFactors %s`.

> outputCheckerboardVolumea pathlike object or string representing an existing file

>   Genete a checkerboard image volume between the fixedVolume and the deformed movingVolume.

> outputDisplacementFieldVolumea pathlike object or string representing an existing file

>   Output deformation field vector image (will have the same physical space as the fixedVolume).

> outputVolumea pathlike object or string representing an existing file

>   Required: output resampled moving image (will have the same physical space as the fixedVolume).