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

Use Cases, Examples

Input Data Requirements

The Atlas Creator expects input data to be structured the following way:

• In general each original image is accompanied by a manual segmentation.
• The images and the segmentations have to be in two different folders but have matching filenames.
• All images and segmentations have to be in Slicer-readable format.
• For Example:
  • ./originals/case1.nrrd
  • ./originals/case2.nrrd
  • ./originals/case3.nrrd
  • ./segmentations/case1.nrrd
  • ./segmentations/case2.nrrd
  • ./segmentations/case3.nrrd

HowTo: Simple Atlas Creation

The following steps perform a Pair Fixed Registration against an automatic chosen template for automatically detected structures.

1. Select the directories containing the Original Images and the Segmentations in the Input/Output panel.

2. Select an Output Directory in the Input/Output panel. It makes sense to create a new directory to use for the Output.

3. Hit Start!

4. After some wait (minutes or hours!, depending on the number of input cases), the generated atlases and the used template will be loaded into 3D Slicer.

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

The Command Line Interface

Beside using the graphical user interface in 3D Slicer, the Atlas Creator can be accessed using the commandline.

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