interfaces.slicer.segmentation.specialized¶
BRAINSROIAuto¶
Wraps the executable command ``BRAINSROIAuto ``.
title: Foreground masking (BRAINS)
category: Segmentation.Specialized
description: This tool uses a combination of otsu thresholding and a closing operations to identify the most prominant foreground region in an image.
version: 2.4.1
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), fedorov -at- bwh.harvard.edu (Slicer integration); (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]
inputVolume: (a pathlike object or string representing an existing
file)
The input image for finding the largest region filled mask.
argument: ``--inputVolume %s``
outputROIMaskVolume: (a boolean or a pathlike object or string
representing a file)
The ROI automatically found from the input image.
argument: ``--outputROIMaskVolume %s``
outputClippedVolumeROI: (a boolean or a pathlike object or string
representing a file)
The inputVolume clipped to the region of the brain mask.
argument: ``--outputClippedVolumeROI %s``
otsuPercentileThreshold: (a float)
Parameter to the Otsu threshold algorithm.
argument: ``--otsuPercentileThreshold %f``
thresholdCorrectionFactor: (a float)
A factor to scale the Otsu algorithm's result threshold, in case
clipping mangles the image.
argument: ``--thresholdCorrectionFactor %f``
closingSize: (a float)
The Closing Size (in millimeters) for largest connected filled mask.
This value is divided by image spacing and rounded to the next
largest voxel number.
argument: ``--closingSize %f``
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``
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``
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:
outputROIMaskVolume: (a pathlike object or string representing an
existing file)
The ROI automatically found from the input image.
outputClippedVolumeROI: (a pathlike object or string representing an
existing file)
The inputVolume clipped to the region of the brain mask.
EMSegmentCommandLine¶
Wraps the executable command ``EMSegmentCommandLine ``.
- title:
- EMSegment Command-line
- category:
- Segmentation.Specialized
- description:
- This module is used to simplify the process of segmenting large collections of images by providing a command line interface to the EMSegment algorithm for script and batch processing.
documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/EMSegment_Command-line
contributor: Sebastien Barre, Brad Davis, Kilian Pohl, Polina Golland, Yumin Yuan, Daniel Haehn
acknowledgements: Many people and organizations have contributed to the funding, design, and development of the EMSegment algorithm and its various implementations.
Inputs:
[Optional]
mrmlSceneFileName: (a pathlike object or string representing an
existing file)
Active MRML scene that contains EMSegment algorithm parameters.
argument: ``--mrmlSceneFileName %s``
resultVolumeFileName: (a boolean or a pathlike object or string
representing a file)
The file name that the segmentation result volume will be written
to.
argument: ``--resultVolumeFileName %s``
targetVolumeFileNames: (a list of items which are a pathlike object
or string representing an existing file)
File names of target volumes (to be segmented). The number of target
images must be equal to the number of target images specified in the
parameter set, and these images must be spatially aligned.
argument: ``--targetVolumeFileNames %s...``
intermediateResultsDirectory: (a pathlike object or string
representing an existing directory)
Directory where EMSegmenter will write intermediate data (e.g.,
aligned atlas data).
argument: ``--intermediateResultsDirectory %s``
parametersMRMLNodeName: (a unicode string)
The name of the EMSegment parameters node within the active MRML
scene. Leave blank for default.
argument: ``--parametersMRMLNodeName %s``
disableMultithreading: (an integer (int or long))
Disable multithreading for the EMSegmenter algorithm only!
Preprocessing might still run in multi-threaded mode. -1: Do not
overwrite default value. 0: Disable. 1: Enable.
argument: ``--disableMultithreading %d``
dontUpdateIntermediateData: (an integer (int or long))
Disable update of intermediate results. -1: Do not overwrite default
value. 0: Disable. 1: Enable.
argument: ``--dontUpdateIntermediateData %d``
verbose: (a boolean)
Enable verbose output.
argument: ``--verbose ``
loadTargetCentered: (a boolean)
Read target files centered.
argument: ``--loadTargetCentered ``
loadAtlasNonCentered: (a boolean)
Read atlas files non-centered.
argument: ``--loadAtlasNonCentered ``
taskPreProcessingSetting: (a unicode string)
Specifies the different task parameter. Leave blank for default.
argument: ``--taskPreProcessingSetting %s``
keepTempFiles: (a boolean)
If flag is set then at the end of command the temporary files are
not removed
argument: ``--keepTempFiles ``
resultStandardVolumeFileName: (a pathlike object or string
representing an existing file)
Used for testing. Compare segmentation results to this image and
return EXIT_FAILURE if they do not match.
argument: ``--resultStandardVolumeFileName %s``
dontWriteResults: (a boolean)
Used for testing. Don't actually write the resulting labelmap to
disk.
argument: ``--dontWriteResults ``
generateEmptyMRMLSceneAndQuit: (a boolean or a pathlike object or
string representing a file)
Used for testing. Only write a scene with default mrml parameters.
argument: ``--generateEmptyMRMLSceneAndQuit %s``
resultMRMLSceneFileName: (a boolean or a pathlike object or string
representing a file)
Write out the MRML scene after command line substitutions have been
made.
argument: ``--resultMRMLSceneFileName %s``
disableCompression: (a boolean)
Don't use compression when writing result image to disk.
argument: ``--disableCompression ``
atlasVolumeFileNames: (a list of items which are a pathlike object or
string representing an existing file)
Use an alternative atlas to the one that is specified by the mrml
file - note the order matters !
argument: ``--atlasVolumeFileNames %s...``
registrationPackage: (a unicode string)
specify the registration package for preprocessing (CMTK or BRAINS
or PLASTIMATCH or DEMONS)
argument: ``--registrationPackage %s``
registrationAffineType: (an integer (int or long))
specify the accuracy of the affine registration. -2: Do not
overwrite default, -1: Test, 0: Disable, 1: Fast, 2: Accurate
argument: ``--registrationAffineType %d``
registrationDeformableType: (an integer (int or long))
specify the accuracy of the deformable registration. -2: Do not
overwrite default, -1: Test, 0: Disable, 1: Fast, 2: Accurate
argument: ``--registrationDeformableType %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:
resultVolumeFileName: (a pathlike object or string representing an
existing file)
The file name that the segmentation result volume will be written
to.
generateEmptyMRMLSceneAndQuit: (a pathlike object or string
representing an existing file)
Used for testing. Only write a scene with default mrml parameters.
resultMRMLSceneFileName: (a pathlike object or string representing an
existing file)
Write out the MRML scene after command line substitutions have been
made.
RobustStatisticsSegmenter¶
Wraps the executable command ``RobustStatisticsSegmenter ``.
title: Robust Statistics Segmenter
category: Segmentation.Specialized
description: Active contour segmentation using robust statistic.
version: 1.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/RobustStatisticsSegmenter
contributor: Yi Gao (gatech), Allen Tannenbaum (gatech), 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
Inputs:
[Optional]
expectedVolume: (a float)
The approximate volume of the object, in mL.
argument: ``--expectedVolume %f``
intensityHomogeneity: (a float)
What is the homogeneity of intensity within the object? Given
constant intensity at 1.0 score and extreme fluctuating intensity at
0.
argument: ``--intensityHomogeneity %f``
curvatureWeight: (a float)
Given sphere 1.0 score and extreme rough bounday/surface 0 score,
what is the expected smoothness of the object?
argument: ``--curvatureWeight %f``
labelValue: (an integer (int or long))
Label value of the output image
argument: ``--labelValue %d``
maxRunningTime: (a float)
The program will stop if this time is reached.
argument: ``--maxRunningTime %f``
originalImageFileName: (a pathlike object or string representing an
existing file)
Original image to be segmented
argument: ``%s``, position: -3
labelImageFileName: (a pathlike object or string representing an
existing file)
Label image for initialization
argument: ``%s``, position: -2
segmentedImageFileName: (a boolean or a pathlike object or string
representing a file)
Segmented image
argument: ``%s``, position: -1
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:
segmentedImageFileName: (a pathlike object or string representing an
existing file)
Segmented image