Modules:AtlasCreator

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AtlasCreator

Atlas Creator User Interface in simple mode

Example of generated Atlases

Comparison of the alignment of two cases before and after Atlas Creation

General Information

Module Type & Category

Type: Built-in Loadable Module

Category: Registration

Authors, Collaborators & Contact

• Daniel Haehn, University of Pennsylvania
• Kilian Pohl, University of Pennsylvania
• Contact: Daniel Haehn (haehn@bwh.harvard.edu)

Module Description

The Atlas Creator module aligns images paired with segmentations to generate statistical atlases for several segmented structures.

Usage

This module supports different usage types:

1. The simple graphical user interface
2. The advanced graphical user interface
3. The command line interface
4. External invocation using the Atlas Creator MRML Node

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

Tutorials

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:

Atlas Creator User Interface in advanced mode

Development

Tests

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

• MyModuleTest1 MyModuleTest1.cxx
• MyModuleTest2 MyModuleTest2.cxx

Source code & documentation

Links to the module's source code:

Source code:

• file.cxx
• file.h

Doxygen documentation:

• class1