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Created page with 'Back to the AtlasCreator documentation.. = AtlasCreator: Commandline Interface = The Atlas Creator comes with a command line interface. This interface …'

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Back to [[Modules:AtlasCreator|the AtlasCreator documentation]]..

= AtlasCreator: Commandline Interface =

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

<pre>
# 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
</pre>

== Help ==

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

<pre>
$ 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!

</pre>

==Examples==

<pre>
$ 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

</pre>

Modules:AtlasCreator:CLI - Revision history

Haehn: Created page with 'Back to the AtlasCreator documentation.. = AtlasCreator: Commandline Interface = The Atlas Creator comes with a command line interface. This interface …'