_               _
| |             (_)
| |__  _ __ __ _ _ _ __  _ __ ___   __ _ ____
| '_ \| '__/ _` | | '_ \| '_ ` _ \ / _` |_  /
| |_) | | | (_| | | | | | | | | | | (_| |/ /
|_.__/|_|  \__,_|_|_| |_|_| |_| |_|\__, /___|
                                    __/ |
                                   |___/

pl-brainmgz

Table of Contents

• pl-brainmgz
  • Abstract
  • Description
  • Usage
    • Arguments
    • Run
  • Development

Abstract

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.

Description

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.

Usage

[python] brainmgz                               \
    [-h|--help]                                 \
    [--json] [--man] [--meta]                   \
    [--savejson <DIR>]                          \
    [-v|--verbosity <level>]                    \
    <inputDir> <outputDir>

Arguments

[-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:

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.

mkdir out && chmod 777 out
docker run --rm                                         \
    -v $(pwd)/out:/outgoing                             \
    fnndsc/pl-brainmgz brainmgz                         \
    /outgoing

Development

Build the Docker container:

docker build -t local/pl-brainmgz .