fnndsc/pl-brainmgz
brainmgz
4.4K
.. code:: console
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.. image:: https://img.shields.io/docker/v/fnndsc/pl-brainmgz?sort=semver :target: https://hub.docker.com/r/fnndsc/pl-brainmgz
.. image:: https://img.shields.io/github/license/fnndsc/pl-brainmgz :target: https://github.com/FNNDSC/pl-brainmgz/blob/master/LICENSE
.. image:: https://github.com/FNNDSC/pl-brainmgz/workflows/ci/badge.svg :target: https://github.com/FNNDSC/pl-brainmgz/actions
.. contents:: Table of Contents
A ChRIS FS app to deliver embedded FreeSurfer brain.mgz
and aparc.*
files to its output directory. These files are made available as part of the Human Connectome Project.
brainmgz
is a ChRIS FS plugin that simply delivers a payload of 25 FreeSurfer brain.mgz
and aparc.*
segmented volume files to its /outgoing
directory.
The primary purpose of this plugin is simply a convenient means to create the root node of a ChRIS feed tree.
.. code::
[python] brainmgz \
[-h|--help] \
[--json] [--man] [--meta] \
[--savejson <DIR>] \
[-v|--verbosity <level>] \
<inputDir> <outputDir>
Arguments
.. code::
[-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-brainmgz brainmgz --man
Run
~~~
If running from the CLI, simply create an output directory and volume map that into the container.
.. code:: bash
mkdir out && chmod 777 out
docker run --rm \
-v $(pwd)/out:/outgoing \
fnndsc/pl-brainmgz brainmgz \
/outgoing
Development
-----------
Build the Docker container:
.. code:: bash
docker build -t local/pl-brainmgz .
.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png
:target: https://chrisstore.co
docker pull fnndsc/pl-brainmgz