Modules:BRAINSROIAuto-Documentation-3.6

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Module Name

BRAINSROIAuto

User Interface

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 uiowa.edu

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.

Usage

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

Development

Notes from the Developer(s)

Dependencies

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

Tests

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.