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

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

• Bug 000: description

Usability issues

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