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.

Features:

• Support for BRAINSFit/CMTK/Congeal toolkits for Registration and Resampling
• Fixed Registration against a template or Dynamic Registration against a mean image
• Normalization of output atlases to a given value
• auto-detection of Structures (labels)
• different Output Casts
• Principal Component Analysis
• Cluster Computation Mode
• using existing Transforms and skipping the Registration (f.e. to re-run a previous generation)

Usage

This module supports different usage types and interfaces:

1. Simple Atlas Creation
2. The extended 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.

Output Directory Structure

The Output Directory contains the following content after the Atlas Creator finished.

• ./template.nrrd - The fixed or dynamic template
• ./normalizedIntensityMapOfAligned.nrrd - An intensity map of all aligned cases, divided by the number of cases.
• ./registered/ - A directory containing the registered Original Images, if Delete Aligned Images is off.
• ./resampled/ - A directory containing the resampled Segmentations used for the Atlas Creation, if Delete Aligned Segs. is off.
• ./transforms/ - A directory containing the generated transforms as a result of the registration
• ./atlasX.nrrd - Atlas for label X, if Activate PCA is off.
• ./atlasY.nrrd - Atlas for label Y, if Activate PCA is off.
• ./atlasZ.nrrd - Atlas for label Z, if Activate PCA is off.
• ./PCA/PCAX/ - A directory containing generated PCA data for label X, if Activate PCA is on.
• ./PCA/PCAY/ - A directory containing generated PCA data for label Y, if Activate PCA is on.
• ./PCA/PCAZ/ - A directory containing generated PCA data for label Z, if Activate PCA is on.
• ... more atlases depending on which structures were used

Quick Tour of Features and Use

The Extended Graphical User Interface

Atlas Creator User Interface in extended mode

The Atlas Creator module is organized in panels from which only the Input/Output panel is expanded by default. Additional features are provided through an extended interface. This extended interface is divided into the Parameters panel and the Advanced panels which are collapsed by default.

Input/Output Panel

• Original Images:
• Segmentations:
• Output directory:
• Registration Type:
  • Pair Fixed:
  • Pair Online:
  • Group Online:

Parameters Panel

• Toolkit:
• Deformation:
  • Affine:
  • Non-rigid:
• Alignment iterations, for Pair Online:
• Default case, for Pair Fixed:

Advanced Panels

Cluster Configuration Panel

The Atlas Creator supports distributing all computations among a Grid Environment.

• Use Cluster:
• Scheduler Command:

Principal Component Analysis Panel

• Activate PCA:
• Max. Eigenvectors:
• Combine PCAs:

Use Existing Transforms Panel

• Skip Registration:
• Transforms directory:
• Existing Template::

Misc. Panel

• Labels:
• Save Transforms:
• Normalize Atlases:
• Normalize to:
• Output cast for Atlases:
• Delete aligned Images:
• Delete aligned Segs.:
• Debug Output:
• Dry-Run (Simulaton):

The Command Line Interface

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

$ cd Slicer3-release/lib/Slicer3/Modules/AtlasCreator/atlascreator.py
$ python atlascreator.py --help
AtlasCreator for 3D Slicer
Version v0.4

Usage:

-h, --help
        Show this information.

-i, --images DIR
        Directory containing original images.

-s, --segmentations DIR
        Directory containing segmentations.

-o, --output DIR
        Output directory.

[....]

The full documentation of the commandline interface is available on a separate page.

Development

Notes from the Developer(s)

Separate notes on the development are available on a separate page.

Dependencies

At least BRAINSFit, CMTK or Congeal have to be installed. BRAINSFit is deployed via Slicer, VMTK and Congeal are available as Slicer extensions.

Tests

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

• vtkMRMLAtlasCreatorNodeTest1 Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeTest1.cxx
• AtlasCreatorLaunchFixedTest Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest1.py
• AtlasCreatorLaunchFixedFailProofTest Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest2.py
• AtlasCreatorLaunchDynamicTest Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest3.py

Usability issues

• Congeal support is still Under Construction.

Source code & documentation

Source code:

• Available in the 3D Slicer Trunk: Modules/AtlasCreator

Doxygen documentation:

• AtlasCreatorGUI
• AtlasCreatorLogic
• AtlasCreatorHelper
• vtkMRMLAtlasCreatorNode

More Information

Please cite this work as:

L. Zöllei, M. Shenton, W.M. Wells III, K.M. Pohl. The Impact of Atlas Formation Methods on Atlas-Guided Brain Segmentation, Statistical Registration. In Pair-wise and Group-wise Alignment and Atlas Formation Workshop at MICCAI 2007: Tenth International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 39 - 46, Brisbane, Australia, 2007

Acknowledgment

The research was funded by an ARRA supplement to NIH NCRR (P41 RR13218).

The Atlas Creator module benefits from several different Toolkits: Thank you for BRAINSTools (Hans Johnson et al.), for CMTK (Torsten Rolfing et al.) and for Congeal (J. De Bonet, L. Zöllei and W.M. Wells III).