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.