pl-fpmmid

Federated Prediction Models for Medical Imaging Data (FPMMID)

Description

FPMMID will provide federated Machine-Learning and Deep-Learning based Prediction Models for a myriad collection of Medical Imaging data from various Data Acquisition systems across the hospital. Currently, FPMMID provides fast-response predictive 4-layer 3D segmentation of individual TW1 MR imaging scans. FPMMID is currently being tested with the PING (Pediatric Imaging, Neurocognition, and Genetics Data Repository) dataset (paper link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4628902/pdf/nihms691152.pdf

pl-fpmmid is a ChRIS ds plugin that wraps around FPMMID.

Installation

pl-fpmmid is a ChRIS plugin, meaning it can run from either within ChRIS or the command-line.

Local Usage

To get started with local command-line usage, use Apptainer (a.k.a. Singularity) to run pl-fpmmid as a container:

singularity exec docker://fnndsc/pl-fpmmid fpmmid [--args values...] input/ output/

To print its available options, run:

singularity exec docker://fnndsc/pl-fpmmid fpmmid --help

Examples

fpmmid requires two positional arguments: a directory containing input data, and a directory where to create output data. First, create the input directory and move input data into it.

mkdir incoming/ outgoing/
mv P0997_t1w.nii.gz  incoming/
singularity exec docker://fnndsc/pl-fpmmid:latest fpmmid incoming/ outgoing/

Development

Instructions for developers.

Building

Build a local container image:

docker build -t localhost/fnndsc/pl-fpmmid .

Running

Mount the source code fpmmid.py into a container to try out changes without rebuild.

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/fpmmid.py:/usr/local/lib/python3.6/dist-packages/fpmmid/fpmmid.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-fpmmid fpmmid /incoming /outgoing

Testing

Run unit tests using nosetests. It's recommended to rebuild the image to ensure that sources are up-to-date.

docker build -t localhost/fnndsc/pl-fpmmid:dev .
docker run --rm -it localhost/fnndsc/pl-fpmmid:dev nosetests

Release

Steps for release can be automated by Github Actions. This section is about how to do those steps manually.

Increase Version Number

Increase the version number in setup.py and commit this file.

Push Container Image

Build and push an image tagged by the version. For example, for version 1.2.3:

docker build -t docker.io/fnndsc/pl-fpmmid:1.2.3 .
docker push docker.io/fnndsc/pl-fpmmid:1.2.3

Get JSON Representation

docker run --rm fnndsc/pl-fpmmid:latest fpmmid --json -> fpmmid.json