interfaces.slicer.registration.specialized¶
ACPCTransform¶
Wraps the executable command ``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.
Inputs:
[Optional]
acpc: (a 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.
argument: ``--acpc %s...``
midline: (a 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).
argument: ``--midline %s...``
outputTransform: (a boolean or a file name)
A transform filled in from the ACPC and Midline registration
calculation
argument: ``--outputTransform %s``
debugSwitch: (a boolean)
Click if wish to see debugging output
argument: ``--debugSwitch ``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
outputTransform: (an existing file name)
A transform filled in from the ACPC and Midline registration
calculation
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://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.
Inputs:
[Optional]
movingVolume: (an existing file name)
Required: input moving image
argument: ``--movingVolume %s``
fixedVolume: (an existing file name)
Required: input fixed (target) image
argument: ``--fixedVolume %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``
outputVolume: (a boolean or a file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
argument: ``--outputVolume %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``
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``
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``
registrationFilterType: ('Demons' or 'FastSymmetricForces' or
'Diffeomorphic')
Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic
argument: ``--registrationFilterType %s``
smoothDisplacementFieldSigma: (a float)
A gaussian smoothing value to be applied to the deformation feild at
each iteration.
argument: ``--smoothDisplacementFieldSigma %f``
numberOfPyramidLevels: (an integer (int or long))
Number of image pyramid levels to use in the multi-resolution
registration.
argument: ``--numberOfPyramidLevels %d``
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``
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``
arrayOfPyramidLevelIterations: (a list of items which are an integer
(int or long))
The number of iterations for each pyramid level
argument: ``--arrayOfPyramidLevelIterations %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 ``
numberOfHistogramBins: (an integer (int or long))
The number of histogram levels
argument: ``--numberOfHistogramBins %d``
numberOfMatchPoints: (an integer (int or long))
The number of match points for histrogramMatch
argument: ``--numberOfMatchPoints %d``
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``
initializeWithDisplacementField: (an existing file name)
Initial deformation field vector image file name
argument: ``--initializeWithDisplacementField %s``
initializeWithTransform: (an existing file name)
Initial Transform filename
argument: ``--initializeWithTransform %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``
fixedBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Fixed image.
argument: ``--fixedBinaryVolume %s``
movingBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Moving image.
argument: ``--movingBinaryVolume %s``
lowerThresholdForBOBF: (an integer (int or long))
Lower threshold for performing BOBF
argument: ``--lowerThresholdForBOBF %d``
upperThresholdForBOBF: (an integer (int or long))
Upper threshold for performing BOBF
argument: ``--upperThresholdForBOBF %d``
backgroundFillValue: (an integer (int or long))
Replacement value to overwrite background when performing BOBF
argument: ``--backgroundFillValue %d``
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``
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``
outputDisplacementFieldPrefix: (a unicode string)
Displacement field filename prefix for writing separate x, y, and z
component images
argument: ``--outputDisplacementFieldPrefix %s``
outputCheckerboardVolume: (a boolean or a file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
argument: ``--outputCheckerboardVolume %s``
checkerboardPatternSubdivisions: (a list of items which are an
integer (int or long))
Number of Checkerboard subdivisions in all 3 directions
argument: ``--checkerboardPatternSubdivisions %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 ``
outputDebug: (a boolean)
Flag to write debugging images after each step.
argument: ``--outputDebug ``
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``
upFieldSmoothing: (a float)
Smoothing sigma for the update field at each iteration
argument: ``--upFieldSmoothing %f``
max_step_length: (a float)
Maximum length of an update vector (0: no restriction)
argument: ``--max_step_length %f``
use_vanilla_dem: (a boolean)
Run vanilla demons algorithm
argument: ``--use_vanilla_dem ``
gui: (a boolean)
Display intermediate image volumes for debugging
argument: ``--gui ``
promptUser: (a boolean)
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer
argument: ``--promptUser ``
numberOfBCHApproximationTerms: (an integer (int or long))
Number of terms in the BCH expansion
argument: ``--numberOfBCHApproximationTerms %d``
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use.
argument: ``--numberOfThreads %d``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
outputVolume: (an existing file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
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.
FiducialRegistration¶
Wraps the executable command ``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.
Inputs:
[Optional]
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...``
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``
rms: (a float)
Display RMS Error.
argument: ``--rms %f``
outputMessage: (a unicode string)
Provides more information on the output
argument: ``--outputMessage %s``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
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://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.
Inputs:
[Optional]
movingVolume: (a list of items which are an existing file name)
Required: input moving image
argument: ``--movingVolume %s...``
fixedVolume: (a list of items which are an existing file name)
Required: input fixed (target) image
argument: ``--fixedVolume %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``
outputVolume: (a boolean or a file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
argument: ``--outputVolume %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``
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``
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``
registrationFilterType: ('Demons' or 'FastSymmetricForces' or
'Diffeomorphic' or 'LogDemons' or 'SymmetricLogDemons')
Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic|L
ogDemons|SymmetricLogDemons
argument: ``--registrationFilterType %s``
smoothDisplacementFieldSigma: (a float)
A gaussian smoothing value to be applied to the deformation feild at
each iteration.
argument: ``--smoothDisplacementFieldSigma %f``
numberOfPyramidLevels: (an integer (int or long))
Number of image pyramid levels to use in the multi-resolution
registration.
argument: ``--numberOfPyramidLevels %d``
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``
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``
arrayOfPyramidLevelIterations: (a list of items which are an integer
(int or long))
The number of iterations for each pyramid level
argument: ``--arrayOfPyramidLevelIterations %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 ``
numberOfHistogramBins: (an integer (int or long))
The number of histogram levels
argument: ``--numberOfHistogramBins %d``
numberOfMatchPoints: (an integer (int or long))
The number of match points for histrogramMatch
argument: ``--numberOfMatchPoints %d``
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``
initializeWithDisplacementField: (an existing file name)
Initial deformation field vector image file name
argument: ``--initializeWithDisplacementField %s``
initializeWithTransform: (an existing file name)
Initial Transform filename
argument: ``--initializeWithTransform %s``
makeBOBF: (a boolean)
Flag to make Brain-Only Background-Filled versions of the input and
target volumes.
argument: ``--makeBOBF ``
fixedBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Fixed image.
argument: ``--fixedBinaryVolume %s``
movingBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Moving image.
argument: ``--movingBinaryVolume %s``
lowerThresholdForBOBF: (an integer (int or long))
Lower threshold for performing BOBF
argument: ``--lowerThresholdForBOBF %d``
upperThresholdForBOBF: (an integer (int or long))
Upper threshold for performing BOBF
argument: ``--upperThresholdForBOBF %d``
backgroundFillValue: (an integer (int or long))
Replacement value to overwrite background when performing BOBF
argument: ``--backgroundFillValue %d``
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``
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``
outputDisplacementFieldPrefix: (a unicode string)
Displacement field filename prefix for writing separate x, y, and z
component images
argument: ``--outputDisplacementFieldPrefix %s``
outputCheckerboardVolume: (a boolean or a file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
argument: ``--outputCheckerboardVolume %s``
checkerboardPatternSubdivisions: (a list of items which are an
integer (int or long))
Number of Checkerboard subdivisions in all 3 directions
argument: ``--checkerboardPatternSubdivisions %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 ``
outputDebug: (a boolean)
Flag to write debugging images after each step.
argument: ``--outputDebug ``
weightFactors: (a list of items which are a float)
Weight fatctors for each input images
argument: ``--weightFactors %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)
argument: ``--gradient_type %s``
upFieldSmoothing: (a float)
Smoothing sigma for the update field at each iteration
argument: ``--upFieldSmoothing %f``
max_step_length: (a float)
Maximum length of an update vector (0: no restriction)
argument: ``--max_step_length %f``
use_vanilla_dem: (a boolean)
Run vanilla demons algorithm
argument: ``--use_vanilla_dem ``
gui: (a boolean)
Display intermediate image volumes for debugging
argument: ``--gui ``
promptUser: (a boolean)
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer
argument: ``--promptUser ``
numberOfBCHApproximationTerms: (an integer (int or long))
Number of terms in the BCH expansion
argument: ``--numberOfBCHApproximationTerms %d``
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use.
argument: ``--numberOfThreads %d``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
outputVolume: (an existing file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
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.