Wraps 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:
[Mandatory]
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
[Optional]
acpc: (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.
args: (a string)
Additional parameters to the command
debugSwitch: (a boolean)
Click if wish to see debugging output
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
midline: (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).
outputTransform: (a boolean or a file name)
A transform filled in from the ACPC and Midline registration
calculation
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
outputTransform: (an existing file name)
A transform filled in from the ACPC and Midline registration
calculation
Wraps command **BRAINSDemonWarp **
title: Demon Registration (BRAINS)
category: Registration.Specialized
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:
[Mandatory]
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
[Optional]
args: (a string)
Additional parameters to the command
arrayOfPyramidLevelIterations: (an integer)
The number of iterations for each pyramid level
backgroundFillValue: (an integer)
Replacement value to overwrite background when performing BOBF
checkerboardPatternSubdivisions: (an integer)
Number of Checkerboard subdivisions in all 3 directions
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
fixedBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Fixed image.
fixedVolume: (an existing file name)
Required: input fixed (target) image
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)
gui: (a boolean)
Display intermediate image volumes for debugging
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.
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
initializeWithDisplacementField: (an existing file name)
Initial deformation field vector image file name
initializeWithTransform: (an existing file name)
Initial Transform filename
inputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
Input volumes will be typecast to this format:
float|short|ushort|int|uchar
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
lowerThresholdForBOBF: (an integer)
Lower threshold for performing BOBF
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.
max_step_length: (a float)
Maximum length of an update vector (0: no restriction)
medianFilterSize: (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.
minimumFixedPyramid: (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)
minimumMovingPyramid: (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)
movingBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Moving image.
movingVolume: (an existing file name)
Required: input moving image
neighborhoodForBOBF: (an integer)
neighborhood in all 3 directions to be included when performing BOBF
numberOfBCHApproximationTerms: (an integer)
Number of terms in the BCH expansion
numberOfHistogramBins: (an integer)
The number of histogram levels
numberOfMatchPoints: (an integer)
The number of match points for histrogramMatch
numberOfPyramidLevels: (an integer)
Number of image pyramid levels to use in the multi-resolution
registration.
numberOfThreads: (an integer)
Explicitly specify the maximum number of threads to use.
outputCheckerboardVolume: (a boolean or a file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
outputDebug: (a boolean)
Flag to write debugging images after each step.
outputDisplacementFieldPrefix: (a string)
Displacement field filename prefix for writing separate x, y, and z
component images
outputDisplacementFieldVolume: (a boolean or a file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
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.
outputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
outputVolume will be typecast to this format:
float|short|ushort|int|uchar
outputVolume: (a boolean or a file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
promptUser: (a boolean)
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer
registrationFilterType: ('Demons' or 'FastSymmetricForces' or
'Diffeomorphic')
Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic
seedForBOBF: (an integer)
coordinates in all 3 directions for Seed when performing BOBF
smoothDisplacementFieldSigma: (a float)
A gaussian smoothing value to be applied to the deformation feild at
each iteration.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
upFieldSmoothing: (a float)
Smoothing sigma for the update field at each iteration
upperThresholdForBOBF: (an integer)
Upper threshold for performing BOBF
use_vanilla_dem: (a boolean)
Run vanilla demons algorithm
Outputs:
outputCheckerboardVolume: (an existing file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
outputDisplacementFieldVolume: (an existing file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
outputVolume: (an existing file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
Wraps 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:
[Mandatory]
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
[Optional]
args: (a string)
Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
fixedLandmarks: (a list of from 3 to 3 items which are a float)
Ordered list of landmarks in the fixed image
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
movingLandmarks: (a list of from 3 to 3 items which are a float)
Ordered list of landmarks in the moving image
outputMessage: (a string)
Provides more information on the output
rms: (a float)
Display RMS Error.
saveTransform: (a boolean or a file name)
Save the transform that results from registration
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
transformType: ('Translation' or 'Rigid' or 'Similarity')
Type of transform to produce
Outputs:
saveTransform: (an existing file name)
Save the transform that results from registration
Wraps command **VBRAINSDemonWarp **
title: Vector Demon Registration (BRAINS)
category: Registration.Specialized
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:
[Mandatory]
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
[Optional]
args: (a string)
Additional parameters to the command
arrayOfPyramidLevelIterations: (an integer)
The number of iterations for each pyramid level
backgroundFillValue: (an integer)
Replacement value to overwrite background when performing BOBF
checkerboardPatternSubdivisions: (an integer)
Number of Checkerboard subdivisions in all 3 directions
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
fixedBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Fixed image.
fixedVolume: (an existing file name)
Required: input fixed (target) image
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)
gui: (a boolean)
Display intermediate image volumes for debugging
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.
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
initializeWithDisplacementField: (an existing file name)
Initial deformation field vector image file name
initializeWithTransform: (an existing file name)
Initial Transform filename
inputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
Input volumes will be typecast to this format:
float|short|ushort|int|uchar
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
lowerThresholdForBOBF: (an integer)
Lower threshold for performing BOBF
makeBOBF: (a boolean)
Flag to make Brain-Only Background-Filled versions of the input and
target volumes.
max_step_length: (a float)
Maximum length of an update vector (0: no restriction)
medianFilterSize: (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.
minimumFixedPyramid: (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)
minimumMovingPyramid: (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)
movingBinaryVolume: (an existing file name)
Mask filename for desired region of interest in the Moving image.
movingVolume: (an existing file name)
Required: input moving image
neighborhoodForBOBF: (an integer)
neighborhood in all 3 directions to be included when performing BOBF
numberOfBCHApproximationTerms: (an integer)
Number of terms in the BCH expansion
numberOfHistogramBins: (an integer)
The number of histogram levels
numberOfMatchPoints: (an integer)
The number of match points for histrogramMatch
numberOfPyramidLevels: (an integer)
Number of image pyramid levels to use in the multi-resolution
registration.
numberOfThreads: (an integer)
Explicitly specify the maximum number of threads to use.
outputCheckerboardVolume: (a boolean or a file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
outputDebug: (a boolean)
Flag to write debugging images after each step.
outputDisplacementFieldPrefix: (a string)
Displacement field filename prefix for writing separate x, y, and z
component images
outputDisplacementFieldVolume: (a boolean or a file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
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.
outputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
outputVolume will be typecast to this format:
float|short|ushort|int|uchar
outputVolume: (a boolean or a file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).
promptUser: (a boolean)
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer
registrationFilterType: ('Demons' or 'FastSymmetricForces' or
'Diffeomorphic' or 'LogDemons' or 'SymmetricLogDemons')
Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic|L
ogDemons|SymmetricLogDemons
seedForBOBF: (an integer)
coordinates in all 3 directions for Seed when performing BOBF
smoothDisplacementFieldSigma: (a float)
A gaussian smoothing value to be applied to the deformation feild at
each iteration.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
upFieldSmoothing: (a float)
Smoothing sigma for the update field at each iteration
upperThresholdForBOBF: (an integer)
Upper threshold for performing BOBF
use_vanilla_dem: (a boolean)
Run vanilla demons algorithm
weightFactors: (a float)
Weight fatctors for each input images
Outputs:
outputCheckerboardVolume: (an existing file name)
Genete a checkerboard image volume between the fixedVolume and the
deformed movingVolume.
outputDisplacementFieldVolume: (an existing file name)
Output deformation field vector image (will have the same physical
space as the fixedVolume).
outputVolume: (an existing file name)
Required: output resampled moving image (will have the same physical
space as the fixedVolume).