.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.slicer.segmentation.specialized
==========================================


.. _nipype.interfaces.slicer.segmentation.specialized.BRAINSROIAuto:


.. index:: BRAINSROIAuto

BRAINSROIAuto
-------------

Code: http://github.com/nipy/nipype/blob/master/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.
