Modules:AtlasCreator:CLI

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AtlasCreator: Commandline Interface

The Atlas Creator comes with a command line interface. This interface can be used by invoking the following command.

# in the source directory
cd Slicer3/Modules/AtlasCreator/

# or in the build directory
cd Slicer3-build/lib/Slicer3/Modules/AtlasCreator/

# start the command line interface
python atlascreator.py

Help

A detailed help system is available by calling python atlascreator.py --help:

$ 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