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# nipype.interfaces.slicer.segmentation.specialized module

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## BRAINSROIAuto

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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)

> ROIAutoDilateSizea 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. Maps to a command-line argument: `--ROIAutoDilateSize %f`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> closingSizea 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. Maps to a command-line argument: `--closingSize %f`.

> environa 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’

>   Environment variables. (Nipype default value: `{}`)

> inputVolumea pathlike object or string representing an existing file

>   The input image for finding the largest region filled mask. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer (int or long)

>   Explicitly specify the maximum number of threads to use. Maps to a command-line argument: `--numberOfThreads %d`.

> otsuPercentileThresholda float

>   Parameter to the Otsu threshold algorithm. Maps to a command-line argument: `--otsuPercentileThreshold %f`.

> outputClippedVolumeROIa boolean or a pathlike object or string representing a file

>   The inputVolume clipped to the region of the brain mask. Maps to a command-line argument: `--outputClippedVolumeROI %s`.

> outputROIMaskVolumea boolean or a pathlike object or string representing a file

>   The ROI automatically found from the input image. Maps to a command-line argument: `--outputROIMaskVolume %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. Maps to a command-line argument: `--outputVolumePixelType %s`.

> thresholdCorrectionFactora float

>   A factor to scale the Otsu algorithm’s result threshold, in case clipping mangles the image. Maps to a command-line argument: `--thresholdCorrectionFactor %f`.

> outputClippedVolumeROIa pathlike object or string representing an existing file

>   The inputVolume clipped to the region of the brain mask.

> outputROIMaskVolumea pathlike object or string representing an existing file

>   The ROI automatically found from the input image.

## EMSegmentCommandLine

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> atlasVolumeFileNamesa 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 ! . Maps to a command-line argument: `--atlasVolumeFileNames %s...`.

> disableCompressiona boolean

>   Don’t use compression when writing result image to disk. Maps to a command-line argument: `--disableCompression`.

> disableMultithreadingan 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. Maps to a command-line argument: `--disableMultithreading %d`.

> dontUpdateIntermediateDataan integer (int or long)

>   Disable update of intermediate results. -1: Do not overwrite default value. 0: Disable. 1: Enable. Maps to a command-line argument: `--dontUpdateIntermediateData %d`.

> dontWriteResultsa boolean

>   Used for testing. Don’t actually write the resulting labelmap to disk. Maps to a command-line argument: `--dontWriteResults`.

> environa 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’

>   Environment variables. (Nipype default value: `{}`)

> generateEmptyMRMLSceneAndQuita boolean or a pathlike object or string representing a file

>   Used for testing. Only write a scene with default mrml parameters. Maps to a command-line argument: `--generateEmptyMRMLSceneAndQuit %s`.

> intermediateResultsDirectorya pathlike object or string representing an existing directory

>   Directory where EMSegmenter will write intermediate data (e.g., aligned atlas data). Maps to a command-line argument: `--intermediateResultsDirectory %s`.

> keepTempFilesa boolean

>   If flag is set then at the end of command the temporary files are not removed. Maps to a command-line argument: `--keepTempFiles`.

> loadAtlasNonCentereda boolean

>   Read atlas files non-centered. Maps to a command-line argument: `--loadAtlasNonCentered`.

> loadTargetCentereda boolean

>   Read target files centered. Maps to a command-line argument: `--loadTargetCentered`.

> mrmlSceneFileNamea pathlike object or string representing an existing file

>   Active MRML scene that contains EMSegment algorithm parameters. Maps to a command-line argument: `--mrmlSceneFileName %s`.

> parametersMRMLNodeNamea unicode string

>   The name of the EMSegment parameters node within the active MRML scene. Leave blank for default. Maps to a command-line argument: `--parametersMRMLNodeName %s`.

> registrationAffineTypean integer (int or long)

>   Specify the accuracy of the affine registration. -2: Do not overwrite default, -1: Test, 0: Disable, 1: Fast, 2: Accurate. Maps to a command-line argument: `--registrationAffineType %d`.

> registrationDeformableTypean integer (int or long)

>   Specify the accuracy of the deformable registration. -2: Do not overwrite default, -1: Test, 0: Disable, 1: Fast, 2: Accurate. Maps to a command-line argument: `--registrationDeformableType %d`.

> registrationPackagea unicode string

>   Specify the registration package for preprocessing (CMTK or BRAINS or PLASTIMATCH or DEMONS). Maps to a command-line argument: `--registrationPackage %s`.

> resultMRMLSceneFileNamea boolean or a pathlike object or string representing a file

>   Write out the MRML scene after command line substitutions have been made. Maps to a command-line argument: `--resultMRMLSceneFileName %s`.

> resultStandardVolumeFileNamea 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. Maps to a command-line argument: `--resultStandardVolumeFileName %s`.

> resultVolumeFileNamea boolean or a pathlike object or string representing a file

>   The file name that the segmentation result volume will be written to. Maps to a command-line argument: `--resultVolumeFileName %s`.

> targetVolumeFileNamesa 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. Maps to a command-line argument: `--targetVolumeFileNames %s...`.

> taskPreProcessingSettinga unicode string

>   Specifies the different task parameter. Leave blank for default. Maps to a command-line argument: `--taskPreProcessingSetting %s`.

> verbosea boolean

>   Enable verbose output. Maps to a command-line argument: `--verbose`.

> generateEmptyMRMLSceneAndQuita pathlike object or string representing an existing file

>   Used for testing. Only write a scene with default mrml parameters.

> resultMRMLSceneFileNamea pathlike object or string representing an existing file

>   Write out the MRML scene after command line substitutions have been made.

> resultVolumeFileNamea pathlike object or string representing an existing file

>   The file name that the segmentation result volume will be written to.

## RobustStatisticsSegmenter

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> curvatureWeighta float

>   Given sphere 1.0 score and extreme rough bounday/surface 0 score, what is the expected smoothness of the object?. Maps to a command-line argument: `--curvatureWeight %f`.

> environa 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’

>   Environment variables. (Nipype default value: `{}`)

> expectedVolumea float

>   The approximate volume of the object, in mL. Maps to a command-line argument: `--expectedVolume %f`.

> intensityHomogeneitya float

>   What is the homogeneity of intensity within the object? Given constant intensity at 1.0 score and extreme fluctuating intensity at 0. Maps to a command-line argument: `--intensityHomogeneity %f`.

> labelImageFileNamea pathlike object or string representing an existing file

>   Label image for initialization. Maps to a command-line argument: `%s` (position: -2).

> labelValuean integer (int or long)

>   Label value of the output image. Maps to a command-line argument: `--labelValue %d`.

> maxRunningTimea float

>   The program will stop if this time is reached. Maps to a command-line argument: `--maxRunningTime %f`.

> originalImageFileNamea pathlike object or string representing an existing file

>   Original image to be segmented. Maps to a command-line argument: `%s` (position: -3).

> segmentedImageFileNamea boolean or a pathlike object or string representing a file

>   Segmented image. Maps to a command-line argument: `%s` (position: -1).

> segmentedImageFileNamea pathlike object or string representing an existing file

>   Segmented image.