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        "author": "Rudolph Pienaar",
        "author_email": "rudolph.pienaar@gmail.com",
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        "description": "pl-freesurfer_pp\n================\n\n.. image:: https://badge.fury.io/py/freesurfer_pp.svg\n    :target: https://badge.fury.io/py/freesurfer_pp\n\n.. image:: https://travis-ci.org/FNNDSC/freesurfer_pp.svg?branch=master\n    :target: https://travis-ci.org/FNNDSC/freesurfer_pp\n\n.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg\n    :target: https://badge.fury.io/py/pl-freesurfer_pp\n\n.. contents:: Table of Contents\n\n\nAbstract\n--------\n\n``freesurfer_pp.py`` is a *dummy* FreeSurfer plugin / container that is prepopulated with the results of several *a priori* FreeSurfer runs. For a given run, this script will simply copy elements of one of these prior runs to the output directory. \n\nSynopsis\n--------\n\n.. code::\n\n        python freesurfer_pp.py                                         \\\n            [-v <level>] [--verbosity <level>]                          \\\n            [--version]                                                 \\\n            [--man]                                                     \\\n            [--meta]                                                    \\\n            [--copySpec <copySpec>]                                     \\\n            [--ageSpec <ageSpec>]                                       \\\n            <inputDir>                                                  \\\n            <outputDir> \n\nRun\n----\n\nThis ``plugin`` can be run in two modes: natively as a python package or as a containerized docker image. The PyPI mode is largely included for completeness sake and only useful if run against some pre-processed tree that exists in the filesystem. \n\nUsing PyPI\n~~~~~~~~~~\n\n*You probably do not want to run the PyPI version unless you are a developer! Mostly likely you want the docker containerized run -- see the next section.*\n\nTo run from PyPI, simply do a \n\n.. code:: bash\n\n    pip install freesurfer_pp\n\nand run with\n\n.. code:: bash\n\n    freesurfer.py --man /tmp /tmp\n\n\nUsing ``docker run``\n~~~~~~~~~~~~~~~~~~~~\n\nThe real utility of this package is to run it containerized against bundled data that is packed into the container.\n\nAssign an \"input\" directory to ``/incoming`` and an \"output\" directory to ``/outgoing``. Note that the \"input\" directory is effectively ignored by this plugin, but is required. Make sure that the host ``$(pwd)/out`` directory is world writable!\n\nIn the simplest sense, the plugin can be run with\n\n.. code:: bash\n\n    mkdir in out && chmod 777 out\n    docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \\\n            fnndsc/pl-freesurfer_pp freesurfer_pp.py                    \\\n            /incoming /outgoing\n\nwhich will copy **only** the internal `stats` directory from a ``10-yr/06-mo/01-da`` subject to the output. By specifying a ``--copySpec stats,3D,sag,cor,tra`` several additional directories containing png image frames through parcellated sagittal, coronal, and transverse (axial) planes as well as multiple 3D images are also copied.\n\nExamples\n--------\n\nCheck available pre-processed runs\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nTo get a listing of the internal tree of already processed and available FreeSurfer choices:\n\n.. code:: bash\n\n    docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \\\n            fnndsc/pl-freesurfer_pp freesurfer_pp.py                    \\\n            -T ../preprocessed                                          \\\n            /incoming /outgoing\n\nThis will print a tree of the available choices of `preprocessed` data in a directory tree. \n\nCopy the default for a selected pre-processed run\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nSelect one run, say the `08-yr/07-mo/16-da` and specify that to copy:\n\n.. code:: bash\n\n    docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \\\n            fnndsc/pl-freesurfer_pp freesurfer_pp.py                    \\\n            -a 08-07-16 \\\n            /incoming /outgoing\n\nSimulate a processing delay\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nTo simulate a processing delay, specify some time in seconds:\n\n.. code:: bash\n\n    docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \\\n            fnndsc/pl-freesurfer_pp freesurfer_pp.py                    \\\n            -a 08-07-16                                                 \\\n            -P 20                                                       \\\n            /incoming /outgoing\n\nExplicitly copy all the data including images from a pre-processed run\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nTo copy all the image directories from the ``10-yr/06-mo/01-da`` subject, \n\n.. code:: bash\n\n    docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \\\n            fnndsc/pl-freesurfer_pp freesurfer_pp.py                    \\\n            -a 10-06-01                                                 \\\n            -c stats,sag,cor,tra,3D                                     \\\n            /incoming /outgoing",
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        "name": "freesurfer-pp",
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