interfaces.slicer.registration.brainsfit¶
BRAINSFit¶
Wraps the executable command ``BRAINSFit ``.
title: General Registration (BRAINS)
category: Registration
description: Register a three-dimensional volume to a reference volume (Mattes Mutual Information by default). Described in BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007. http://hdl.handle.net/1926/1291
version: 3.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit
license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
contributor: Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu
acknowledgements: Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3); Andriy Fedorov(5) 1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard
Inputs:
[Optional]
fixedVolume: (an existing file name)
The fixed image for registration by mutual information optimization.
argument: ``--fixedVolume %s``
movingVolume: (an existing file name)
The moving image for registration by mutual information
optimization.
argument: ``--movingVolume %s``
bsplineTransform: (a boolean or a file name)
(optional) Filename to which save the estimated transform. NOTE: You
must set at least one output object (either a deformed image or a
transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS BSpline
argument: ``--bsplineTransform %s``
linearTransform: (a boolean or a file name)
(optional) Filename to which save the estimated transform. NOTE: You
must set at least one output object (either a deformed image or a
transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS ---NOT---
BSpline
argument: ``--linearTransform %s``
outputVolume: (a boolean or a file name)
(optional) Output image for registration. NOTE: You must select
either the outputTransform or the outputVolume option.
argument: ``--outputVolume %s``
initialTransform: (an existing file name)
Filename of transform used to initialize the registration. This CAN
NOT be used with either CenterOfHeadLAlign, MomentsAlign,
GeometryAlign, or initialTransform file.
argument: ``--initialTransform %s``
initializeTransformMode: ('Off' or 'useMomentsAlign' or
'useCenterOfHeadAlign' or 'useGeometryAlign' or
'useCenterOfROIAlign')
Determine how to initialize the transform center. GeometryAlign on
assumes that the center of the voxel lattice of the images represent
similar structures. MomentsAlign assumes that the center of mass of
the images represent similar structures. useCenterOfHeadAlign
attempts to use the top of head and shape of neck to drive a center
of mass estimate. Off assumes that the physical space of the images
are close, and that centering in terms of the image Origins is a
good starting point. This flag is mutually exclusive with the
initialTransform flag.
argument: ``--initializeTransformMode %s``
useRigid: (a boolean)
Perform a rigid registration as part of the sequential registration
steps. This family of options superceeds the use of transformType if
any of them are set.
argument: ``--useRigid ``
useScaleVersor3D: (a boolean)
Perform a ScaleVersor3D registration as part of the sequential
registration steps. This family of options superceeds the use of
transformType if any of them are set.
argument: ``--useScaleVersor3D ``
useScaleSkewVersor3D: (a boolean)
Perform a ScaleSkewVersor3D registration as part of the sequential
registration steps. This family of options superceeds the use of
transformType if any of them are set.
argument: ``--useScaleSkewVersor3D ``
useAffine: (a boolean)
Perform an Affine registration as part of the sequential
registration steps. This family of options superceeds the use of
transformType if any of them are set.
argument: ``--useAffine ``
useBSpline: (a boolean)
Perform a BSpline registration as part of the sequential
registration steps. This family of options superceeds the use of
transformType if any of them are set.
argument: ``--useBSpline ``
numberOfSamples: (an integer (int or long))
The number of voxels sampled for mutual information computation.
Increase this for a slower, more careful fit. You can also limit the
sampling focus with ROI masks and ROIAUTO mask generation.
argument: ``--numberOfSamples %d``
splineGridSize: (a list of items which are an integer (int or long))
The number of subdivisions of the BSpline Grid to be centered on the
image space. Each dimension must have at least 3 subdivisions for
the BSpline to be correctly computed.
argument: ``--splineGridSize %s``
numberOfIterations: (a list of items which are an integer (int or
long))
The maximum number of iterations to try before failing to converge.
Use an explicit limit like 500 or 1000 to manage risk of divergence
argument: ``--numberOfIterations %s``
maskProcessingMode: ('NOMASK' or 'ROIAUTO' or 'ROI')
What mode to use for using the masks. If ROIAUTO is choosen, then
the mask is implicitly defined using a otsu forground and hole
filling algorithm. The Region Of Interest mode (choose ROI) uses the
masks to define what parts of the image should be used for computing
the transform.
argument: ``--maskProcessingMode %s``
fixedBinaryVolume: (an existing file name)
Fixed Image binary mask volume, ONLY FOR MANUAL ROI mode.
argument: ``--fixedBinaryVolume %s``
movingBinaryVolume: (an existing file name)
Moving Image binary mask volume, ONLY FOR MANUAL ROI mode.
argument: ``--movingBinaryVolume %s``
outputFixedVolumeROI: (a boolean or a file name)
The ROI automatically found in fixed image, ONLY FOR ROIAUTO mode.
argument: ``--outputFixedVolumeROI %s``
outputMovingVolumeROI: (a boolean or a file name)
The ROI automatically found in moving image, ONLY FOR ROIAUTO mode.
argument: ``--outputMovingVolumeROI %s``
outputVolumePixelType: ('float' or 'short' or 'ushort' or 'int' or
'uint' or 'uchar')
The output image Pixel Type is the scalar datatype for
representation of the Output Volume.
argument: ``--outputVolumePixelType %s``
backgroundFillValue: (a float)
Background fill value for output image.
argument: ``--backgroundFillValue %f``
maskInferiorCutOffFromCenter: (a float)
For use with --useCenterOfHeadAlign (and --maskProcessingMode
ROIAUTO): the cut-off below the image centers, in millimeters,
argument: ``--maskInferiorCutOffFromCenter %f``
scaleOutputValues: (a boolean)
If true, and the voxel values do not fit within the minimum and
maximum values of the desired outputVolumePixelType, then linearly
scale the min/max output image voxel values to fit within the
min/max range of the outputVolumePixelType.
argument: ``--scaleOutputValues ``
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, NearestNeighbor, BSpline, WindowedSinc,
or ResampleInPlace. The ResampleInPlace option will create an image
with the same discrete voxel values and will adjust the origin and
direction of the physical space interpretation.
argument: ``--interpolationMode %s``
minimumStepLength: (a list of items which are a float)
Each step in the optimization takes steps at least this big. When
none are possible, registration is complete.
argument: ``--minimumStepLength %s``
translationScale: (a float)
How much to scale up changes in position compared to unit rotational
changes in radians -- decrease this to put more rotation in the
search pattern.
argument: ``--translationScale %f``
reproportionScale: (a float)
ScaleVersor3D 'Scale' compensation factor. Increase this to put more
rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern.
1.0 works well with a translationScale of 1000.0
argument: ``--reproportionScale %f``
skewScale: (a float)
ScaleSkewVersor3D Skew compensation factor. Increase this to put
more skew in a ScaleSkewVersor3D search pattern. 1.0 works well with
a translationScale of 1000.0
argument: ``--skewScale %f``
maxBSplineDisplacement: (a float)
Sets the maximum allowed displacements in image physical
coordinates for BSpline control grid along each axis. A value of 0.0
indicates that the problem should be unbounded. NOTE: This only
constrains the BSpline portion, and does not limit the displacement
from the associated bulk transform. This can lead to a substantial
reduction in computation time in the BSpline optimizer.,
argument: ``--maxBSplineDisplacement %f``
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. Do NOT use if registering images from
different modailties.
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
argument: ``--numberOfMatchPoints %d``
strippedOutputTransform: (a boolean or a file name)
File name for the rigid component of the estimated affine transform.
Can be used to rigidly register the moving image to the fixed image.
NOTE: This value is overwritten if either bsplineTransform or
linearTransform is set.
argument: ``--strippedOutputTransform %s``
transformType: (a list of items which are a unicode string)
Specifies a list of registration types to be used. The valid types
are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline.
Specifiying more than one in a comma separated list will initialize
the next stage with the previous results. If registrationClass flag
is used, it overrides this parameter setting.
argument: ``--transformType %s``
outputTransform: (a boolean or a file name)
(optional) Filename to which save the (optional) estimated
transform. NOTE: You must select either the outputTransform or the
outputVolume option.
argument: ``--outputTransform %s``
fixedVolumeTimeIndex: (an integer (int or long))
The index in the time series for the 3D fixed image to fit, if
4-dimensional.
argument: ``--fixedVolumeTimeIndex %d``
movingVolumeTimeIndex: (an integer (int or long))
The index in the time series for the 3D moving image to fit, if
4-dimensional.
argument: ``--movingVolumeTimeIndex %d``
medianFilterSize: (a list of items which are an integer (int or
long))
The radius for the optional MedianImageFilter preprocessing in all 3
directions.
argument: ``--medianFilterSize %s``
removeIntensityOutliers: (a float)
The half percentage to decide outliers of image intensities. The
default value is zero, which means no outlier removal. If the value
of 0.005 is given, the moduel will throw away 0.005 % of both tails,
so 0.01% of intensities in total would be ignored in its statistic
calculation.
argument: ``--removeIntensityOutliers %f``
useCachingOfBSplineWeightsMode: ('ON' or 'OFF')
This is a 5x speed advantage at the expense of requiring much more
memory. Only relevant when transformType is BSpline.
argument: ``--useCachingOfBSplineWeightsMode %s``
useExplicitPDFDerivativesMode: ('AUTO' or 'ON' or 'OFF')
Using mode AUTO means OFF for BSplineDeformableTransforms and ON for
the linear transforms. The ON alternative uses more memory to
sometimes do a better job.
argument: ``--useExplicitPDFDerivativesMode %s``
ROIAutoDilateSize: (a float)
This flag is only relavent when using ROIAUTO mode for initializing
masks. It defines the final dilation size to capture a bit of
background outside the tissue region. At setting of 10mm has been
shown to help regularize a BSpline registration type so that there
is some background constraints to match the edges of the head
better.
argument: ``--ROIAutoDilateSize %f``
ROIAutoClosingSize: (a float)
This flag is only relavent when using ROIAUTO mode for initializing
masks. It defines the hole closing size in mm. It is rounded up to
the nearest whole pixel size in each direction. The default is to
use a closing size of 9mm. For mouse data this value may need to be
reset to 0.9 or smaller.
argument: ``--ROIAutoClosingSize %f``
relaxationFactor: (a float)
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future.
argument: ``--relaxationFactor %f``
maximumStepLength: (a float)
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future.
argument: ``--maximumStepLength %f``
failureExitCode: (an integer (int or long))
If the fit fails, exit with this status code. (It can be used to
force a successfult exit status of (0) if the registration fails due
to reaching the maximum number of iterations.
argument: ``--failureExitCode %d``
writeTransformOnFailure: (a boolean)
Flag to save the final transform even if the numberOfIterations are
reached without convergence. (Intended for use when
--failureExitCode 0 )
argument: ``--writeTransformOnFailure ``
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use. (default is
auto-detected)
argument: ``--numberOfThreads %d``
forceMINumberOfThreads: (an integer (int or long))
Force the the maximum number of threads to use for non thread safe
MI metric. CAUTION: Inconsistent results my arise!
argument: ``--forceMINumberOfThreads %d``
debugLevel: (an integer (int or long))
Display debug messages, and produce debug intermediate results.
0=OFF, 1=Minimal, 10=Maximum debugging.
argument: ``--debugLevel %d``
costFunctionConvergenceFactor: (a float)
From itkLBFGSBOptimizer.h: Set/Get the
CostFunctionConvergenceFactor. Algorithm terminates when the
reduction in cost function is less than (factor * epsmcj) where
epsmch is the machine precision. Typical values for factor: 1e+12
for low accuracy; 1e+7 for moderate accuracy and 1e+1 for extremely
high accuracy. 1e+9 seems to work well.,
argument: ``--costFunctionConvergenceFactor %f``
projectedGradientTolerance: (a float)
From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance.
Algorithm terminates when the project gradient is below the
tolerance. Default lbfgsb value is 1e-5, but 1e-4 seems to work
well.,
argument: ``--projectedGradientTolerance %f``
gui: (a boolean)
Display intermediate image volumes for debugging. NOTE: This is not
part of the standard build sytem, and probably does nothing on your
installation.
argument: ``--gui ``
promptUser: (a boolean)
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer
argument: ``--promptUser ``
NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00: (a boolean)
DO NOT USE THIS FLAG
argument: ``--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00 ``
NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01: (a boolean)
DO NOT USE THIS FLAG
argument: ``--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01 ``
NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02: (a boolean)
DO NOT USE THIS FLAG
argument: ``--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02 ``
permitParameterVariation: (a list of items which are an integer (int
or long))
A bit vector to permit linear transform parameters to vary under
optimization. The vector order corresponds with transform
parameters, and beyond the end ones fill in as a default. For
instance, you can choose to rotate only in x (pitch) with 1,0,0;
this is mostly for expert use in turning on and off individual
degrees of freedom in rotation, translation or scaling without
multiplying the number of transform representations; this trick is
probably meaningless when tried with the general affine transform.
argument: ``--permitParameterVariation %s``
costMetric: ('MMI' or 'MSE' or 'NC' or 'MC')
The cost metric to be used during fitting. Defaults to MMI. Options
are MMI (Mattes Mutual Information), MSE (Mean Square Error), NC
(Normalized Correlation), MC (Match Cardinality for binary images)
argument: ``--costMetric %s``
writeOutputTransformInFloat: (a boolean)
By default, the output registration transforms (either the output
composite transform or each transform component) are written to the
disk in double precision. If this flag is ON, the output transforms
will be written in single (float) precision. It is especially
important if the output transform is a displacement field transform,
or it is a composite transform that includes several displacement
fields.
argument: ``--writeOutputTransformInFloat ``
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:
bsplineTransform: (an existing file name)
(optional) Filename to which save the estimated transform. NOTE: You
must set at least one output object (either a deformed image or a
transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS BSpline
linearTransform: (an existing file name)
(optional) Filename to which save the estimated transform. NOTE: You
must set at least one output object (either a deformed image or a
transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS ---NOT---
BSpline
outputVolume: (an existing file name)
(optional) Output image for registration. NOTE: You must select
either the outputTransform or the outputVolume option.
outputFixedVolumeROI: (an existing file name)
The ROI automatically found in fixed image, ONLY FOR ROIAUTO mode.
outputMovingVolumeROI: (an existing file name)
The ROI automatically found in moving image, ONLY FOR ROIAUTO mode.
strippedOutputTransform: (an existing file name)
File name for the rigid component of the estimated affine transform.
Can be used to rigidly register the moving image to the fixed image.
NOTE: This value is overwritten if either bsplineTransform or
linearTransform is set.
outputTransform: (an existing file name)
(optional) Filename to which save the (optional) estimated
transform. NOTE: You must select either the outputTransform or the
outputVolume option.