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
  • different Output Casts
  • PCA Analysis
  • Cluster Computation
  • 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.

Quick Tour of Features and Use

The Extended Graphical User Interface

The Atlas Creator provides additional features through an extended interface. This interface is divided into the Parameters panel and the Advanced panel.
Atlas Creator User Interface in extended mode

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.

A help system is available: 

$ 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.

--cmtk
        Use the CMTK toolkit for registration and resampling, instead of BRAINSFit.
        The CMTK4Slicer extensions have to be installed in order to use CMTK.

--skipRegistration
        Skip the registration and use existing transforms.

        The following arguments have to be specified if the registration is skipped:

        --transforms DIR
                Directory containing existing transforms.

        --existingTemplate FILEPATH
                Filepath to an existing template used for resampling only.

--dynamic
        Use a dynamic template for registration based on means of images.

        The following arguments have to be specified if dynamic registration is chosen:

        -m, --meanIterations INT
                Number of iterations to compute and register against a mean image.

--fixed
        Use a fixed template for registration.

        The following arguments have to be specified if fixed registration is chosen:

        --template FILEPATH
                Filepath to an image used as a template for fixed registration.

        --ignoreTemplateSegmentation
                If activated, the template's segmentation will not be added to the atlases.

-n, --non-rigid
        Use Non-Rigid registration additionally.

-w, --writeTransforms
        Write transforms to output directory.

--keepAligned
        Keep the aligned images and segmentations.

-l, --labels STRING
        List of labels to include for the atlases, f.e. "3 4 5 6 8 10".
        DEFAULT: detect labels automatically

--normalize
        Normalize Atlases to 0..1.
        If activated, the output cast will be set to Double.

        --normalizeTo INT
                The upper value to normalize the atlases to.
                DEFAULT: 1

--outputCast INT
        Output cast for the atlases. Possible values:
        0: Char
        1: Unsigned Char
        2: Double
        3: Float
        4: Int
        5: Unsigned Int
        6: Long
        7: Unsigned Long
        8: Short
        9: Unsigned Short
        DEFAULT: 8

-c, --cluster
        Use the cluster mode.

        The following arguments have to be specified if cluster mode is chosen:

        --schedulerCommand EXECUTABLE
                The executable to use as a scheduler in cluster mode, f.e. "qsub".

--pca
        Perform PCA Analysis on top of Resampling.

        --pcaMaxEigenVectors INT
                The number of maximal Eigenvectors to use for model generation.
                DEFAULT: 10

        --pcaCombine
                Combine the PCA output.

--slicer FILEPATH
        Filepath to the 3D Slicer launcher including arguments, f.e. "/usr/bin/Slicer3 --tmp_dir /var/tmp".
        DEFAULT: Find the 3D Slicer launcher automatically.

-d, --debug
        Enable debug information.

--dryrun
        Output executable commands instead of running the registration or resampling.

--examples
        Show usage examples.


Developed by Daniel Haehn and Kilian Pohl, University of Pennsylvania. The research was funded by an ARRA supplement to NIH NCRR (P41 RR13218).

Thanks to everyone!

Examples: 

$ python atlascreator.py --examples
AtlasCreator for 3D Slicer
Version v0.4

Examples:
-----------------------------------------------------------------------------------------------
1. Run fixed registration with the testdata and normalize the atlases to 1:

        python atlascreator.py -i TestData/originals/ -s TestData/segmentations/ -o /tmp/acout --fixed --template TestData/originals/case62.nrrd -w -l "3 4 5 6 7 8 9" --normalize

-----------------------------------------------------------------------------------------------
2. Run fixed registration with the testdata and use CMTK instead of BRAINSFit and label auto-detection:

        python atlascreator.py -i TestData/originals/ -s TestData/segmentations/ -o /tmp/acout --fixed --template TestData/originals/case62.nrrd -w --cmtk

-----------------------------------------------------------------------------------------------
3. Run dynamic registration with the testdata and normalize the atlases to 0..100:

        python atlascreator.py -i TestData/originals/ -s TestData/segmentations/ -o /tmp/acout --dynamic --meanIterations 5 -w -l "3 4 5 6 7 8 9" --normalize --normalizeTo 100

-----------------------------------------------------------------------------------------------
4. Run dynamic registration with the testdata on a cluster (scheduler command "qsub -l centos5"):

        python atlascreator.py -i TestData/originals/ -s TestData/segmentations/ -o /tmp/acout --dynamic --meanIterations 5 -w -l "3 4 5 6 7 8 9" --normalize --cluster --schedulerCommand "qsub -l centos5"

-----------------------------------------------------------------------------------------------
5. Use existing registrations and just re-sample

        python atlascreator.py --skipRegistration --transforms /tmp/acout --existingTemplate TestData/segmentations/case62.nrrd -s TestData/segmentations/ -o /tmp/acout -l "3 4 5 6 7 8 9" --normalize --outputCast 3

Development

Notes from the Developer(s)

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

Dependencies

Tests

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

Known bugs

Usability issues

Source code & documentation

Source code:

Doxygen documentation:

More Information

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 to Hans Johnson et al. for BRAINSFit, Torsten Rolfing et al. for CMTK and Jeremy De Bonet et al. for Congeal.

References

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