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Gallery of New Features

Module Name


User Interface

General Information

Module Type & Category

Type: CLI

Category: Segmentation

Authors, Collaborators & Contact

Author: Hans J. Johnson, hans-johnson -at-,

Contributors: Hans Johnson(1,3,4); (1=University of Iowa Department of Psychiatry, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering)

Module Description

Program title BRAINSROIAuto - Foreground masking tool
Program version 2.4.1
Program documentation-url


BRAINSROIAuto finds the foreground tissue region in an image.

  • IO
    • Input Image Volume [--inputVolume] : The input image for finding the largest region filled mask.
    • Output Mask [--outputROIMaskVolume] : The ROI automatically found from the input image.
    • Output Image Clipped by ROI [--outputClippedVolumeROI] : The inputVolume clipped to the region of the brain mask.

  • Configuration Parameters
    • Otsu Percentile Threshold [--otsuPercentileThreshold] : Parameter to the Otsu threshold algorithm. Default value: 0.01
    • Otsu Correction Factor [--thresholdCorrectionFactor] : A factor to scale the Otsu algorithm's result threshold, in case clipping mangles the image. Default value: 1.0
    • Closing Size [--closingSize] : 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. Default value: 9.0
    • ROIAuto Dilate Size [--ROIAutoDilateSize] : 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. Default value: 0.0
    • Output Image Pixel Type [--outputVolumePixelType] : The output image Pixel Type is the scalar datatype for representation of the Output Volume. Default value: short


Quick Tour of Features and Use


Notes from the Developer(s)


BRAINSROIAuto depends on Slicer3 (for the SlicerExecutionModel support) and ITK. BRAINSROIAuto depends on BRAINSCommonLib


Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

More Information


The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.


Publications related to this module go here. Links to pdfs would be useful. -->