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interfaces.slicer.segmentation.specialized

BRAINSROIAuto

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/segmentation/specialized.py#L28

Wraps command ** BRAINSROIAuto **

title: Foreground masking (BRAINS)

category: Segmentation.Specialized

description: This program is used to create a mask over the most prominant forground region in an image. This is accomplished via a combination of otsu thresholding and a closing operation. More documentation is available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Modules/ForegroundMasking.

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.
args: (a string)
        Additional parameters to the command
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.
cropOutput: (a boolean)
        The inputVolume cropped to the region of the ROI mask.
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.
maskOutput: (a boolean)
        The inputVolume multiplied by the ROI mask.
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
otsuPercentileThreshold: (a float)
        Parameter to the Otsu threshold algorithm.
outputROIMaskVolume: (a boolean or a file name)
        The ROI automatically found from the input image.
outputVolume: (a boolean or a file name)
        The inputVolume with optional [maskOutput|cropOutput] to the region of the brain mask.
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.
thresholdCorrectionFactor: (a float)
        A factor to scale the Otsu algorithm's result threshold, in case clipping mangles the
        image.

Outputs:

outputROIMaskVolume: (an existing file name)
        The ROI automatically found from the input image.
outputVolume: (an existing file name)
        The inputVolume with optional [maskOutput|cropOutput] to the region of the brain mask.