bids-client

Holding place for BIDS enabled client REF: https://flywheelio.aha.io/epics/FW-E-39

Overview

The BIDS Client has three components:

• Upload
• Curate
• Export

Below is more information about each of the components.

Build the image

The following command will build the docker image containing all BIDS Client components.

git clone https://github.com/flywheel-io/bids-client
cd bids-client
docker build -t flywheel/bids-client .

Upload

The upload script (upload_bids.py) takes a BIDS dataset and uploads it to Flywheel.

Flywheel CLI

NOTE: This requires the Flywheel CLI.

The upload script has been integrated into the flywheel cli as

fw import bids [folder] [group] [project] [flags]

Docker Script

A docker script has been provided to simplify the below process. To run:

./docker/upload.sh \
    /path/to/BIDS/dir/in/container \
    --api-key '<PLACE YOUR API KEY HERE>' \
    --type 'Flywheel' \
    -g '<PLACE GROUP ID HERE>'

An optional project flag can also be given if the given BIDS directory is not at the project level.

    -p '<PLACE PROJECT LABEL HERE>'

Run Docker image locally

Startup container

docker run -it --rm \
    -v /path/to/BIDS/dir/locally:/path/to/BIDS/dir/in/container \
     bids-client /bin/bash

Run the upload script

python /code/upload_bids.py \
    --bids-dir /path/to/BIDS/dir/in/container \
    --api-key '<PLACE YOUR API KEY HERE>' \
    --type 'Flywheel' \
    -g '<PLACE GROUP ID HERE>'

Curate

Gear

The BIDS Curation step (curate_bids.py) has been transformed into a gear for better usability. The git repo for the gear is here: https://github.com/flywheel-apps/curate-bids

Docker Script

Run it using the docker script

./docker/curate.sh \
    --api-key '<PLACE YOUR API KEY HERE>' \
    -p '<PLACE PROJECT LABEL HERE>' \
    [optional flags]

Flags:

  --reset               Reset BIDS data before running
  --template-file       Template file to use

Export

The export script (export_bids.py) takes a curated dataset within Flywheel and downloads it to local disk.

Flywheel CLI

NOTE: This requires the Flywheel CLI.

Usage:

fw export bids [dest folder] [flags]

Flags:

  -h, --help             help for bids
  -p, --project string   The label of the project to export
      --source-data      Include sourcedata in BIDS export

Docker Script

To run

./docker/export.sh \
    /path/to/BIDS/dir/in/container \
    --api-key '<PLACE YOUR API KEY HERE>' \
    -p '<PLACE PROJECT LABEL HERE>'

Run Docker image locally

Startup container

docker run -it --rm \
    -v /path/to/BIDS/dir/locally:/path/to/BIDS/dir/in/container \
     bids-client /bin/bash

Run the export script

python /code/export_bids.py \
    --bids-dir /path/to/BIDS/dir/in/container \
    --api-key '<PLACE YOUR API KEY HERE>' \
    -p '<PROJECT LABEL TO DOWNLOAD>'