interfaces.semtools.registration.specialized¶
BRAINSDemonWarp¶
Wraps the executable command `` 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.
Inputs:
[Optional]
minimumFixedPyramid: (a 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)
argument: ``--minimumFixedPyramid %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.
argument: ``--outputNormalized ``
checkerboardPatternSubdivisions: (a list of items which are an
integer (int or long))
Number of Checkerboard subdivisions in all 3 directions
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', nipype default value: {})
Environment variables
lowerThresholdForBOBF: (an integer (int or long))
Lower threshold for performing BOBF
argument: ``--lowerThresholdForBOBF %d``
numberOfBCHApproximationTerms: (an integer (int or long))
Number of terms in the BCH expansion
argument: ``--numberOfBCHApproximationTerms %d``
movingVolume: (an existing file name)
Required: input moving image
argument: ``--movingVolume %s``
minimumMovingPyramid: (a 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)
argument: ``--minimumMovingPyramid %s``
movingBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Moving image.
argument: ``--movingBinaryVolume %s``
numberOfMatchPoints: (an integer (int or long))
The number of match points for histrogramMatch
argument: ``--numberOfMatchPoints %d``
upperThresholdForBOBF: (an integer (int or long))
Upper threshold for performing BOBF
argument: ``--upperThresholdForBOBF %d``
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)
argument: ``--gradient_type %s``
outputDisplacementFieldPrefix: (a unicode string)
Displacement field filename prefix for writing separate x, y, and z
component images
argument: ``--outputDisplacementFieldPrefix %s``
inputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
Input volumes will be typecast to this format:
float|short|ushort|int|uchar
argument: ``--inputPixelType %s``
outputDebug: (a boolean)
Flag to write debugging images after each step.
argument: ``--outputDebug ``
initializeWithDisplacementField: (an existing file name)
Initial deformation field vector image file name
argument: ``--initializeWithDisplacementField %s``
outputDisplacementFieldVolume: (a boolean or a file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
argument: ``--outputDisplacementFieldVolume %s``
numberOfHistogramBins: (an integer (int or long))
The number of histogram levels
argument: ``--numberOfHistogramBins %d``
fixedBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Fixed image.
argument: ``--fixedBinaryVolume %s``
smoothDisplacementFieldSigma: (a float)
A gaussian smoothing value to be applied to the deformation feild at
each iteration.
argument: ``--smoothDisplacementFieldSigma %f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
use_vanilla_dem: (a boolean)
Run vanilla demons algorithm
argument: ``--use_vanilla_dem ``
max_step_length: (a float)
Maximum length of an update vector (0: no restriction)
argument: ``--max_step_length %f``
registrationFilterType: ('Demons' or 'FastSymmetricForces' or
'Diffeomorphic')
Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic
argument: ``--registrationFilterType %s``
outputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
outputVolume will be typecast to this format:
float|short|ushort|int|uchar
argument: ``--outputPixelType %s``
backgroundFillValue: (an integer (int or long))
Replacement value to overwrite background when performing BOBF
argument: ``--backgroundFillValue %d``
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
argument: ``--interpolationMode %s``
upFieldSmoothing: (a float)
Smoothing sigma for the update field at each iteration
argument: ``--upFieldSmoothing %f``
numberOfPyramidLevels: (an integer (int or long))
Number of image pyramid levels to use in the multi-resolution
registration.
argument: ``--numberOfPyramidLevels %d``
promptUser: (a boolean)
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer
argument: ``--promptUser ``
seedForBOBF: (a list of items which are an integer (int or long))
coordinates in all 3 directions for Seed when performing BOBF
argument: ``--seedForBOBF %s``
arrayOfPyramidLevelIterations: (a list of items which are an integer
(int or long))
The number of iterations for each pyramid level
argument: ``--arrayOfPyramidLevelIterations %s``
initializeWithTransform: (an existing file name)
Initial Transform filename
argument: ``--initializeWithTransform %s``
gui: (a boolean)
Display intermediate image volumes for debugging
argument: ``--gui ``
neighborhoodForBOBF: (a list of items which are an integer (int or
long))
neighborhood in all 3 directions to be included when performing BOBF
argument: ``--neighborhoodForBOBF %s``
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.
argument: ``--histogramMatch ``
outputCheckerboardVolume: (a boolean or a file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
argument: ``--outputCheckerboardVolume %s``
outputVolume: (a boolean or a file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
argument: ``--outputVolume %s``
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.
argument: ``--maskProcessingMode %s``
fixedVolume: (an existing file name)
Required: input fixed (target) image
argument: ``--fixedVolume %s``
medianFilterSize: (a 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.
argument: ``--medianFilterSize %s``
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use.
argument: ``--numberOfThreads %d``
Outputs:
outputDisplacementFieldVolume: (an existing file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
outputCheckerboardVolume: (an existing file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
outputVolume: (an existing file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
BRAINSTransformFromFiducials¶
Wraps the executable command `` 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.
Inputs:
[Optional]
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
saveTransform: (a boolean or a file name)
Save the transform that results from registration
argument: ``--saveTransform %s``
transformType: ('Translation' or 'Rigid' or 'Similarity')
Type of transform to produce
argument: ``--transformType %s``
movingLandmarksFile: (an existing file name)
An fcsv formatted file with a list of landmark points.
argument: ``--movingLandmarksFile %s``
fixedLandmarksFile: (an existing file name)
An fcsv formatted file with a list of landmark points.
argument: ``--fixedLandmarksFile %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', nipype default value: {})
Environment variables
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
argument: ``--fixedLandmarks %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
argument: ``--movingLandmarks %s...``
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use.
argument: ``--numberOfThreads %d``
Outputs:
saveTransform: (an existing file name)
Save the transform that results from registration
VBRAINSDemonWarp¶
Wraps the executable command `` 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.
Inputs:
[Optional]
minimumFixedPyramid: (a 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)
argument: ``--minimumFixedPyramid %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.
argument: ``--outputNormalized ``
checkerboardPatternSubdivisions: (a list of items which are an
integer (int or long))
Number of Checkerboard subdivisions in all 3 directions
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', nipype default value: {})
Environment variables
lowerThresholdForBOBF: (an integer (int or long))
Lower threshold for performing BOBF
argument: ``--lowerThresholdForBOBF %d``
numberOfBCHApproximationTerms: (an integer (int or long))
Number of terms in the BCH expansion
argument: ``--numberOfBCHApproximationTerms %d``
movingVolume: (a list of items which are an existing file name)
Required: input moving image
argument: ``--movingVolume %s...``
minimumMovingPyramid: (a 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)
argument: ``--minimumMovingPyramid %s``
movingBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Moving image.
argument: ``--movingBinaryVolume %s``
makeBOBF: (a boolean)
Flag to make Brain-Only Background-Filled versions of the input and
target volumes.
argument: ``--makeBOBF ``
numberOfMatchPoints: (an integer (int or long))
The number of match points for histrogramMatch
argument: ``--numberOfMatchPoints %d``
upperThresholdForBOBF: (an integer (int or long))
Upper threshold for performing BOBF
argument: ``--upperThresholdForBOBF %d``
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)
argument: ``--gradient_type %s``
outputDisplacementFieldPrefix: (a unicode string)
Displacement field filename prefix for writing separate x, y, and z
component images
argument: ``--outputDisplacementFieldPrefix %s``
inputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
Input volumes will be typecast to this format:
float|short|ushort|int|uchar
argument: ``--inputPixelType %s``
outputDebug: (a boolean)
Flag to write debugging images after each step.
argument: ``--outputDebug ``
initializeWithDisplacementField: (an existing file name)
Initial deformation field vector image file name
argument: ``--initializeWithDisplacementField %s``
outputDisplacementFieldVolume: (a boolean or a file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
argument: ``--outputDisplacementFieldVolume %s``
numberOfHistogramBins: (an integer (int or long))
The number of histogram levels
argument: ``--numberOfHistogramBins %d``
fixedBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Fixed image.
argument: ``--fixedBinaryVolume %s``
smoothDisplacementFieldSigma: (a float)
A gaussian smoothing value to be applied to the deformation feild at
each iteration.
argument: ``--smoothDisplacementFieldSigma %f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
use_vanilla_dem: (a boolean)
Run vanilla demons algorithm
argument: ``--use_vanilla_dem ``
max_step_length: (a float)
Maximum length of an update vector (0: no restriction)
argument: ``--max_step_length %f``
registrationFilterType: ('Demons' or 'FastSymmetricForces' or
'Diffeomorphic' or 'LogDemons' or 'SymmetricLogDemons')
Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic|L
ogDemons|SymmetricLogDemons
argument: ``--registrationFilterType %s``
outputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
outputVolume will be typecast to this format:
float|short|ushort|int|uchar
argument: ``--outputPixelType %s``
backgroundFillValue: (an integer (int or long))
Replacement value to overwrite background when performing BOBF
argument: ``--backgroundFillValue %d``
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
argument: ``--interpolationMode %s``
upFieldSmoothing: (a float)
Smoothing sigma for the update field at each iteration
argument: ``--upFieldSmoothing %f``
numberOfPyramidLevels: (an integer (int or long))
Number of image pyramid levels to use in the multi-resolution
registration.
argument: ``--numberOfPyramidLevels %d``
promptUser: (a boolean)
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer
argument: ``--promptUser ``
seedForBOBF: (a list of items which are an integer (int or long))
coordinates in all 3 directions for Seed when performing BOBF
argument: ``--seedForBOBF %s``
arrayOfPyramidLevelIterations: (a list of items which are an integer
(int or long))
The number of iterations for each pyramid level
argument: ``--arrayOfPyramidLevelIterations %s``
initializeWithTransform: (an existing file name)
Initial Transform filename
argument: ``--initializeWithTransform %s``
gui: (a boolean)
Display intermediate image volumes for debugging
argument: ``--gui ``
neighborhoodForBOBF: (a list of items which are an integer (int or
long))
neighborhood in all 3 directions to be included when performing BOBF
argument: ``--neighborhoodForBOBF %s``
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.
argument: ``--histogramMatch ``
outputCheckerboardVolume: (a boolean or a file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
argument: ``--outputCheckerboardVolume %s``
outputVolume: (a boolean or a file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
argument: ``--outputVolume %s``
weightFactors: (a list of items which are a float)
Weight fatctors for each input images
argument: ``--weightFactors %s``
fixedVolume: (a list of items which are an existing file name)
Required: input fixed (target) image
argument: ``--fixedVolume %s...``
medianFilterSize: (a 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.
argument: ``--medianFilterSize %s``
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use.
argument: ``--numberOfThreads %d``
Outputs:
outputDisplacementFieldVolume: (an existing file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
outputCheckerboardVolume: (an existing file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
outputVolume: (an existing file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).