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Module Name


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General Information

Module Type & Category

Type: CLI

Category: Registration

Authors, Collaborators & Contact

  • Author1: Hans Johnson, University of Iowa
  • Contributor1: Kent WIlliams, University of Iowa
  • Contact: Hans Johnson, hans-johson at

Module Description

BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain.


In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

Quick Tour of Features and Use

  • IO Parameters
    • Input Image Volume: Image for which mask should be generated
    • Output Mask: Output binary image volume, defining the mask.
    • Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.
  • Configuration Parameters
    • Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
    • Otsu Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
    • Closing Size: The size for the largest void to fill in the mask, in voxels.
    • Output Image Pixel Type: the scalar type of the masked output volume.
User Interface


Notes from the Developer(s)


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


TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.

Known bugs

Links to known bugs in the Slicer3 bug tracker

Usability issues

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

<!== ===Source code & documentation===

Links to the module's source code:

Source code:

Doxygen documentation:

More Information


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