nipype.interfaces.semtools.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.
BRAINSDemonWarp¶
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://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSDemonWarp.
version: 3.0.0
documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/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.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.arrayOfPyramidLevelIterations (a list of items which are an integer) – The number of iterations for each pyramid level. Maps to a command-line argument:
--arrayOfPyramidLevelIterations %s.backgroundFillValue (an integer) – Replacement value to overwrite background when performing BOBF. Maps to a command-line argument:
--backgroundFillValue %d.checkerboardPatternSubdivisions (a list of items which are an integer) – Number of Checkerboard subdivisions in all 3 directions. Maps to a command-line argument:
--checkerboardPatternSubdivisions %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:
{})fixedBinaryVolume (a 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.fixedVolume (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.gui (a boolean) – Display intermediate image volumes for debugging. Maps to a command-line argument:
--gui.histogramMatch (a 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.initializeWithDisplacementField (a pathlike object or string representing an existing file) – Initial deformation field vector image file name. Maps to a command-line argument:
--initializeWithDisplacementField %s.initializeWithTransform (a 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.lowerThresholdForBOBF (an integer) – 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 chosen, then the mask is implicitly defined using a otsu foreground 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_length (a float) – Maximum length of an update vector (0: no restriction). Maps to a command-line argument:
--max_step_length %f.medianFilterSize (a list of items which are an integer) – 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.minimumFixedPyramid (a list of items which are an integer) – 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.minimumMovingPyramid (a list of items which are an integer) – 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.movingBinaryVolume (a 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.movingVolume (a pathlike object or string representing an existing file) – Required: input moving image. Maps to a command-line argument:
--movingVolume %s.neighborhoodForBOBF (a list of items which are an integer) – Neighborhood in all 3 directions to be included when performing BOBF. Maps to a command-line argument:
--neighborhoodForBOBF %s.numberOfBCHApproximationTerms (an integer) – Number of terms in the BCH expansion. Maps to a command-line argument:
--numberOfBCHApproximationTerms %d.numberOfHistogramBins (an integer) – The number of histogram levels. Maps to a command-line argument:
--numberOfHistogramBins %d.numberOfMatchPoints (an integer) – The number of match points for histrogramMatch. Maps to a command-line argument:
--numberOfMatchPoints %d.numberOfPyramidLevels (an integer) – Number of image pyramid levels to use in the multi-resolution registration. Maps to a command-line argument:
--numberOfPyramidLevels %d.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputCheckerboardVolume (a 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.outputDebug (a boolean) – Flag to write debugging images after each step. Maps to a command-line argument:
--outputDebug.outputDisplacementFieldPrefix (a string) – Displacement field filename prefix for writing separate x, y, and z component images. Maps to a command-line argument:
--outputDisplacementFieldPrefix %s.outputDisplacementFieldVolume (a 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.outputNormalized (a 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.outputVolume (a 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.promptUser (a 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.seedForBOBF (a list of items which are an integer) – Coordinates in all 3 directions for Seed when performing BOBF. Maps to a command-line argument:
--seedForBOBF %s.smoothDisplacementFieldSigma (a float) – A gaussian smoothing value to be applied to the deformation field at each iteration. Maps to a command-line argument:
--smoothDisplacementFieldSigma %f.upFieldSmoothing (a float) – Smoothing sigma for the update field at each iteration. Maps to a command-line argument:
--upFieldSmoothing %f.upperThresholdForBOBF (an integer) – Upper threshold for performing BOBF. Maps to a command-line argument:
--upperThresholdForBOBF %d.use_vanilla_dem (a boolean) – Run vanilla demons algorithm. Maps to a command-line argument:
--use_vanilla_dem.- Outputs:
outputCheckerboardVolume (a pathlike object or string representing an existing file) – Genete a checkerboard image volume between the fixedVolume and the deformed movingVolume.
outputDisplacementFieldVolume (a pathlike object or string representing an existing file) – Output deformation field vector image (will have the same physical space as the fixedVolume).
outputVolume (a pathlike object or string representing an existing file) – Required: output resampled moving image (will have the same physical space as the fixedVolume).
BRAINSTransformFromFiducials¶
Bases: SEMLikeCommandLine
Wrapped executable:
BRAINSTransformFromFiducials.title: Fiducial Registration (BRAINS)
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://www.slicer.org/slicerWiki/index.php/Modules:TransformFromFiducials-Documentation-3.6
contributor: Casey B Goodlett
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.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%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:
{})fixedLandmarks (a 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....fixedLandmarksFile (a pathlike object or string representing an existing file) – An fcsv formatted file with a list of landmark points. Maps to a command-line argument:
--fixedLandmarksFile %s.movingLandmarks (a 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....movingLandmarksFile (a pathlike object or string representing an existing file) – An fcsv formatted file with a list of landmark points. Maps to a command-line argument:
--movingLandmarksFile %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.saveTransform (a 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.- Outputs:
saveTransform (a pathlike object or string representing an existing file) – Save the transform that results from registration.
VBRAINSDemonWarp¶
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://www.slicer.org/slicerWiki/index.php/Documentation/4.1/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.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.arrayOfPyramidLevelIterations (a list of items which are an integer) – The number of iterations for each pyramid level. Maps to a command-line argument:
--arrayOfPyramidLevelIterations %s.backgroundFillValue (an integer) – Replacement value to overwrite background when performing BOBF. Maps to a command-line argument:
--backgroundFillValue %d.checkerboardPatternSubdivisions (a list of items which are an integer) – Number of Checkerboard subdivisions in all 3 directions. Maps to a command-line argument:
--checkerboardPatternSubdivisions %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:
{})fixedBinaryVolume (a 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.fixedVolume (a 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.gui (a boolean) – Display intermediate image volumes for debugging. Maps to a command-line argument:
--gui.histogramMatch (a 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.initializeWithDisplacementField (a pathlike object or string representing an existing file) – Initial deformation field vector image file name. Maps to a command-line argument:
--initializeWithDisplacementField %s.initializeWithTransform (a 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.lowerThresholdForBOBF (an integer) – Lower threshold for performing BOBF. Maps to a command-line argument:
--lowerThresholdForBOBF %d.makeBOBF (a boolean) – Flag to make Brain-Only Background-Filled versions of the input and target volumes. Maps to a command-line argument:
--makeBOBF.max_step_length (a float) – Maximum length of an update vector (0: no restriction). Maps to a command-line argument:
--max_step_length %f.medianFilterSize (a list of items which are an integer) – 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.minimumFixedPyramid (a list of items which are an integer) – 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.minimumMovingPyramid (a list of items which are an integer) – 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.movingBinaryVolume (a 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.movingVolume (a 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....neighborhoodForBOBF (a list of items which are an integer) – Neighborhood in all 3 directions to be included when performing BOBF. Maps to a command-line argument:
--neighborhoodForBOBF %s.numberOfBCHApproximationTerms (an integer) – Number of terms in the BCH expansion. Maps to a command-line argument:
--numberOfBCHApproximationTerms %d.numberOfHistogramBins (an integer) – The number of histogram levels. Maps to a command-line argument:
--numberOfHistogramBins %d.numberOfMatchPoints (an integer) – The number of match points for histrogramMatch. Maps to a command-line argument:
--numberOfMatchPoints %d.numberOfPyramidLevels (an integer) – Number of image pyramid levels to use in the multi-resolution registration. Maps to a command-line argument:
--numberOfPyramidLevels %d.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputCheckerboardVolume (a 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.outputDebug (a boolean) – Flag to write debugging images after each step. Maps to a command-line argument:
--outputDebug.outputDisplacementFieldPrefix (a string) – Displacement field filename prefix for writing separate x, y, and z component images. Maps to a command-line argument:
--outputDisplacementFieldPrefix %s.outputDisplacementFieldVolume (a 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.outputNormalized (a 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.outputVolume (a 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.promptUser (a 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.seedForBOBF (a list of items which are an integer) – Coordinates in all 3 directions for Seed when performing BOBF. Maps to a command-line argument:
--seedForBOBF %s.smoothDisplacementFieldSigma (a float) – A gaussian smoothing value to be applied to the deformation field at each iteration. Maps to a command-line argument:
--smoothDisplacementFieldSigma %f.upFieldSmoothing (a float) – Smoothing sigma for the update field at each iteration. Maps to a command-line argument:
--upFieldSmoothing %f.upperThresholdForBOBF (an integer) – Upper threshold for performing BOBF. Maps to a command-line argument:
--upperThresholdForBOBF %d.use_vanilla_dem (a boolean) – Run vanilla demons algorithm. Maps to a command-line argument:
--use_vanilla_dem.weightFactors (a list of items which are a float) – Weight fatctors for each input images. Maps to a command-line argument:
--weightFactors %s.- Outputs:
outputCheckerboardVolume (a pathlike object or string representing an existing file) – Genete a checkerboard image volume between the fixedVolume and the deformed movingVolume.
outputDisplacementFieldVolume (a pathlike object or string representing an existing file) – Output deformation field vector image (will have the same physical space as the fixedVolume).
outputVolume (a pathlike object or string representing an existing file) – Required: output resampled moving image (will have the same physical space as the fixedVolume).