interfaces.slicer.segmentation.specialized

BRAINSROIAuto

Link to code

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: (an existing file name)
        The input image for finding the largest region filled mask.
        argument: ``--inputVolume %s``
outputROIMaskVolume: (a boolean or a file name)
        The ROI automatically found from the input image.
        argument: ``--outputROIMaskVolume %s``
outputClippedVolumeROI: (a boolean or a file name)
        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: (an existing file name)
        The ROI automatically found from the input image.
outputClippedVolumeROI: (an existing file name)
        The inputVolume clipped to the region of the brain mask.

EMSegmentCommandLine

Link to code

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: (an existing file name)
        Active MRML scene that contains EMSegment algorithm parameters.
        argument: ``--mrmlSceneFileName %s``
resultVolumeFileName: (a boolean or a file name)
        The file name that the segmentation result volume will be written
        to.
        argument: ``--resultVolumeFileName %s``
targetVolumeFileNames: (a list of items which are an existing file
          name)
        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: (an existing directory name)
        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: (an existing file name)
        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 file name)
        Used for testing. Only write a scene with default mrml parameters.
        argument: ``--generateEmptyMRMLSceneAndQuit %s``
resultMRMLSceneFileName: (a boolean or a file name)
        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 an existing file
          name)
        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: (an existing file name)
        The file name that the segmentation result volume will be written
        to.
generateEmptyMRMLSceneAndQuit: (an existing file name)
        Used for testing. Only write a scene with default mrml parameters.
resultMRMLSceneFileName: (an existing file name)
        Write out the MRML scene after command line substitutions have been
        made.

RobustStatisticsSegmenter

Link to code

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: (an existing file name)
        Original image to be segmented
        argument: ``%s``, position: -3
labelImageFileName: (an existing file name)
        Label image for initialization
        argument: ``%s``, position: -2
segmentedImageFileName: (a boolean or a file name)
        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: (an existing file name)
        Segmented image