interfaces.slicer.segmentation.specialized¶
BRAINSROIAuto¶
Wraps 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:
[Mandatory]
[Optional]
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.
flag: --ROIAutoDilateSize %f
args: (a string)
Additional parameters to the command
flag: %s
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.
flag: --closingSize %f
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
inputVolume: (an existing file name)
The input image for finding the largest region filled mask.
flag: --inputVolume %s
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use.
flag: --numberOfThreads %d
otsuPercentileThreshold: (a float)
Parameter to the Otsu threshold algorithm.
flag: --otsuPercentileThreshold %f
outputClippedVolumeROI: (a boolean or a file name)
The inputVolume clipped to the region of the brain mask.
flag: --outputClippedVolumeROI %s
outputROIMaskVolume: (a boolean or a file name)
The ROI automatically found from the input image.
flag: --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.
flag: --outputVolumePixelType %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
thresholdCorrectionFactor: (a float)
A factor to scale the Otsu algorithm's result threshold, in case
clipping mangles the image.
flag: --thresholdCorrectionFactor %f
Outputs:
outputClippedVolumeROI: (an existing file name)
The inputVolume clipped to the region of the brain mask.
outputROIMaskVolume: (an existing file name)
The ROI automatically found from the input image.
EMSegmentCommandLine¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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 !
flag: --atlasVolumeFileNames %s...
disableCompression: (a boolean)
Don't use compression when writing result image to disk.
flag: --disableCompression
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.
flag: --disableMultithreading %d
dontUpdateIntermediateData: (an integer (int or long))
Disable update of intermediate results. -1: Do not overwrite default
value. 0: Disable. 1: Enable.
flag: --dontUpdateIntermediateData %d
dontWriteResults: (a boolean)
Used for testing. Don't actually write the resulting labelmap to
disk.
flag: --dontWriteResults
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
generateEmptyMRMLSceneAndQuit: (a boolean or a file name)
Used for testing. Only write a scene with default mrml parameters.
flag: --generateEmptyMRMLSceneAndQuit %s
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
intermediateResultsDirectory: (an existing directory name)
Directory where EMSegmenter will write intermediate data (e.g.,
aligned atlas data).
flag: --intermediateResultsDirectory %s
keepTempFiles: (a boolean)
If flag is set then at the end of command the temporary files are
not removed
flag: --keepTempFiles
loadAtlasNonCentered: (a boolean)
Read atlas files non-centered.
flag: --loadAtlasNonCentered
loadTargetCentered: (a boolean)
Read target files centered.
flag: --loadTargetCentered
mrmlSceneFileName: (an existing file name)
Active MRML scene that contains EMSegment algorithm parameters.
flag: --mrmlSceneFileName %s
parametersMRMLNodeName: (a string)
The name of the EMSegment parameters node within the active MRML
scene. Leave blank for default.
flag: --parametersMRMLNodeName %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
flag: --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
flag: --registrationDeformableType %d
registrationPackage: (a string)
specify the registration package for preprocessing (CMTK or BRAINS
or PLASTIMATCH or DEMONS)
flag: --registrationPackage %s
resultMRMLSceneFileName: (a boolean or a file name)
Write out the MRML scene after command line substitutions have been
made.
flag: --resultMRMLSceneFileName %s
resultStandardVolumeFileName: (an existing file name)
Used for testing. Compare segmentation results to this image and
return EXIT_FAILURE if they do not match.
flag: --resultStandardVolumeFileName %s
resultVolumeFileName: (a boolean or a file name)
The file name that the segmentation result volume will be written
to.
flag: --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.
flag: --targetVolumeFileNames %s...
taskPreProcessingSetting: (a string)
Specifies the different task parameter. Leave blank for default.
flag: --taskPreProcessingSetting %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
verbose: (a boolean)
Enable verbose output.
flag: --verbose
Outputs:
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.
resultVolumeFileName: (an existing file name)
The file name that the segmentation result volume will be written
to.
RobustStatisticsSegmenter¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
curvatureWeight: (a float)
Given sphere 1.0 score and extreme rough bounday/surface 0 score,
what is the expected smoothness of the object?
flag: --curvatureWeight %f
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
expectedVolume: (a float)
The approximate volume of the object, in mL.
flag: --expectedVolume %f
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
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.
flag: --intensityHomogeneity %f
labelImageFileName: (an existing file name)
Label image for initialization
flag: %s, position: -2
labelValue: (an integer (int or long))
Label value of the output image
flag: --labelValue %d
maxRunningTime: (a float)
The program will stop if this time is reached.
flag: --maxRunningTime %f
originalImageFileName: (an existing file name)
Original image to be segmented
flag: %s, position: -3
segmentedImageFileName: (a boolean or a file name)
Segmented image
flag: %s, position: -1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
segmentedImageFileName: (an existing file name)
Segmented image