pl-mri_sag_anon_192

Table of Contents

• Abstract
• Description
• Usage
  • Arguments
  • Run
• Development
• Examples
  • Copy DCM files

Abstract

This application copies a set of image slices to the output directory.

Description

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.

Usage

mri_sag_anon_192                                            \
    [--dir <dirToCopy>                                      \
    [-h|--help]                                             \
    [--json] [--man] [--meta]                               \
    [--savejson <DIR>]                                      \
    [-v|--verbosity <level>]                                \
    [--version]                                             \
    <outputDir>

Arguments

[--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:

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.

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:

docker build -t local/pl-mri_sag_anon_192 .

Run unit tests:

docker run --rm local/pl-mri_sag_anon_192 nosetests

Examples

Copy DCM files

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