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UNDER CONSTRUCTION - extension file is not checked in to Slicer 3.6 branch nor trunk yet.



SPECTRE User Interface
Output - Brain mask split at midsagittal plane overlaid on original image.
Output - Skullstripped results.

General Information

Module Type & Category

Type: Extension

Category: Segmentation

Authors, Collaborators & Contact

  • Nicole Aucoin, BWH
  • Min Chen, JHU
  • Aaron Carass, JHU
  • Contact: Nicole Aucoin, Min Chen

Module Description

Overview of what the module does goes here.


Use Cases, Examples

This module is especially appropriate for these use cases:

  • Use Case 1:
  • Use Case 2:

Examples of the module in use:

  • Example 1
  • Example 2


Links to tutorials explaining how to use this module:

  • Tutorial 1
    • Data Set 1

Quick Tour of Features and Use

A list panels in the interface, their features, what they mean, and how to use them. For instance:

  • Main Panel:
    • Input volume
    • Atlas List
    • Initial Erosion distance
    • Image Modality
    • Output in Original Image Space
    • Find Midsaggital Plane
  • Advanced panel:
    • Run Smooth Brain Mask
    • Resample Data to Isotropic Voxels
    • Initial Probability Threshold
    • Minimum Probability threshold
    • MMC Dilation Distance
    • MMC Erosion Distance
  • FANTASM panel:
    • Inhomogeneity Correction
    • Smoothing Parameter
    • Background Threshold (%)
  • MSP panel:
    • Output Plane?
    • Output Split-Halves?
    • Output Segmentation on Plane?
  • Optimized Automated Registration panel:
    • Main Subpanel
      • Degres of freedom
      • Cost Function
      • Registration Interpolation
      • Output Interpolation
      • Apply Rotation
      • Minimum Angle
      • Maximum Angle
      • Coarse Angle Increment
      • Fine Angle Increment
    • Advanced Subpanel
      • Multiple of Tolerance to Bracket the Minimum
      • Number of Iterations
      • Number of Minima From Level 8 to test at Level 4
      • Use the Max of the Min Resolutions of the Two Datasets when Resampling
      • Subsample Image for Speed
      • Skip Multilevel Search (Assume Images are Close to Alignment)
      • Multithreading for Registration
  • Output panel:
    • First output
    • Second output
  • Viewing panel:
SPECTRE User Interface (full)


Notes from the Developer(s)

Algorithms used, library classes depended upon, use cases, etc.


Other modules or packages that are required for this module's use.


On the Dashboard, these tests verify that the module is working on various platforms:

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


Include funding and other support here.


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