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An anonymized MRI exemplar

Project description

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Abstract

This application simply copies from embedded data a reference normal anonymized MRI of a subject aged 10 years, 06 months, 01 days.

Synopsis

mri10yr06mo01da_normal.python                                   \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    [--dir <dir>]                                               \
    [--splash <splash>]                                         \
    <outputDir>

Arguments

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--version]
If specified, print version number.

[--man]
If specified, print this man page.

[--meta]
If specified, print plugin meta data.

[--splash <splash>]
An optional splash message to print on startup.

[--dir <dir>]
An optional override directory to copy to the <outputDir>.
Note, if run from a containerized version, this will copy
a directory from the *container* file system.

Run

This plugin can be run in two modes: natively as a python package or as a containerized docker image.

Using PyPI

To run from PyPI, simply do a

pip install mri10yr06mo01da_normal

and run with

mri10yr06mo01da_normal.py --man /tmp

to get inline help. The app should also understand being called with only one positional argument

mri10yr06mo01da_normal.py /destination/directory

Using docker run

To run using docker, be sure to assign an “input” directory to /incoming and an output directory to /outgoing. Make sure that the $(pwd)/out directory is world writable!

Now, prefix all calls with

docker run --rm -v $(pwd)/out:/outgoing                             \
        fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py                        \

Thus, getting inline help is:

mkdir out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py  \
        --man                                                       \
        /outgoing

Examples

Copy the embedded MRI data to the out directory

mkdir out && chmod 777 out
docker run --rm -v $(pwd)/out:/outgoing                             \
        fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py  \
        /outgoing

Copy a user specified directory to the out directory

mkdir out && chmod 777 out
docker run --rm -v $(pwd)/out:/outgoing                             \
        fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py  \
        --dir /usr/src/data
        /outgoing

Project details


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