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A simple/dummy app that simulates a FreeSurfer run

Project description

Abstract 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.


python                                         \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    [--copySpec <copySpec>]                                     \
    [--ageSpec <ageSpec>]                                       \
    <inputDir>                                                  \


This 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.

Using PyPI

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.

To run from PyPI, simply do a

pip install freesurfer_pp

and run with --man /tmp /tmp

Using docker run

The real utility of this package is to run it containerized against bundled data that is packed into the container.

Assign 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!

In the simplest sense, the plugin can be run with

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

which 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.


Check available pre-processed runs

To get a listing of the internal tree of already processed and available FreeSurfer choices:

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-freesurfer_pp                    \
        -T ../preprocessed                                          \
        /incoming /outgoing

This will print a tree of the available choices of preprocessed data in a directory tree.

Copy the default for a selected pre-processed run

Select one run, say the 08-yr/07-mo/16-da and specify that to copy:

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-freesurfer_pp                    \
        -a 08-07-16 \
        /incoming /outgoing

Simulate a processing delay

To simulate a processing delay, specify some time in seconds:

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-freesurfer_pp                    \
        -a 08-07-16                                                 \
        -P 20                                                       \
        /incoming /outgoing

Explicitly copy all the data including images from a pre-processed run

To copy all the image directories from the 10-yr/06-mo/01-da subject,

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-freesurfer_pp                    \
        -a 10-06-01                                                 \
        -c stats,sag,cor,tra,3D                                     \
        /incoming /outgoing

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