fnndsc/pl-mri_sag_anon_192
Anonymous sagittal neuro MRI image set of 192 slices
3.5K
.. image:: https://img.shields.io/docker/v/fnndsc/pl-mri_sag_anon_192?sort=semver :target: https://hub.docker.com/r/fnndsc/pl-mri_sag_anon_192
.. image:: https://img.shields.io/github/license/fnndsc/pl-mri_sag_anon_192 :target: https://github.com/FNNDSC/pl-mri_sag_anon_192/blob/master/LICENSE
.. image:: https://github.com/FNNDSC/pl-mri_sag_anon_192/workflows/ci/badge.svg :target: https://github.com/FNNDSC/pl-mri_sag_anon_192/actions
.. contents:: Table of Contents
This application copies a set of image slices to the output directory.
mri_sag_anon_192.py
copies a "built-in" set of anonymized neuro MRI images that are bundled within the container to the output directory.
The plugin is a convenient delivery platform for a creating a new Feed with a set of MRI data suitable for further analysis.
.. code::
mri_sag_anon_192 \
[--dir <dirToCopy> \
[-h|--help] \
[--json] [--man] [--meta] \
[--savejson <DIR>] \
[-v|--verbosity <level>] \
[--version] \
<outputDir>
Arguments
.. code::
[--dir <directoryToCopyToOutput>]
A directory to copy to the <outputDir>. Note that it you are
running this as a container, then this path is a path located
_within the container_!
For the containerized build, the default path is
/usr/local/src/data/dcm
An addition path is also available
/usr/local/src/data/nii
[-h] [--help]
If specified, show help message and exit.
[--json]
If specified, show json representation of app and exit.
[--man]
If specified, print (this) man page and exit.
[--meta]
If specified, print plugin meta data and exit.
[--savejson <DIR>]
If specified, save json representation file to DIR and exit.
[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.
[--version]
If specified, print version number and exit.
Getting inline help is:
.. code:: bash
docker run --rm fnndsc/pl-mri_sag_anon_192 mri_sag_anon_192 --man
Run
~~~
You need you need to specify input and output directories using the `-v` flag to `docker run`.
.. code:: bash
docker run --rm -u $(id -u) \
-v $(pwd)/out:/outgoing \
fnndsc/pl-mri_sag_anon_192 mri_sag_anon_192 \
/outgoing
Development
-----------
Build the Docker container:
.. code:: bash
docker build -t local/pl-mri_sag_anon_192 .
Run unit tests:
.. code:: bash
docker run --rm local/pl-mri_sag_anon_192 nosetests
Examples
--------
Copy DCM files
.. code:: bash
docker run --rm -u $(id -u) \
-v $(pwd)/out:/outgoing \
fnndsc/pl-mri_sag_anon_192 mri_sag_anon_192 \
/outgoing
Copy a NIfTI volume:
docker run --rm -u $(id -u) \
-v $(pwd)/out:/outgoing \
fnndsc/pl-mri_sag_anon_192 mri_sag_anon_192 \
--dir /usr/local/src/data/nii \
/outgoing
.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png :target: https://chrisstore.co
docker pull fnndsc/pl-mri_sag_anon_192