Command-Line Interface Overview

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Introduction

The Command-Line Interface (CLI) provides a powerful way to interact with Flywheel. This document provides an overview of the features of the Flywheel CLI along with some examples.

Download the Flywheel CLI

See our article to download and install the Flywheel CLI.

Command

Description

batch

Start or manage server batch jobs

bids

Run the BIDS validator on a directory

See our BIDS import or BIDS export articles for more information.

cp

Copy a local file to a remote location, or vice-a-versa

deid

Create and test de-identification template

download

Download a remote file or container.

See our article for steps for running this command.

export

Export BIDS data from Flywheel. Use the download command for other datatypes.

gear

Gear commands (requires Docker).

See our gear documentation for more information on using this command.

help

Help about any command

import

Import data into Flywheel.

See our import dicom, import template, import folder , import PAR/REC, import bruker for more information.

Ingest

Create and test de-identification template

See our ingest dicom, ingest folder, or ingest template articles for more information.

job

Start or manage server jobs

login

Login to a Flywheel instance

logout

Delete your saved API key

ls

Show remote files

status

See your current login status

sync

Sync files from Flywheel to storage

See our article for more information

upload

Upload a remote file

version

Print CLI version

 

Getting Help

With any command, one can add -h or --help to get more information. Below is an example of what one should see with the ls command. 

Help

$ fw ls -h
Show remote files

Usage:
  fw ls [path] [flags]

Flags:
  -h, --help   help for ls
      --ids    Display database identifiers

Navigating your Flywheel Instance from the CLI

We can start with fw ls . This lists the groups available to you and your current permission level.

ls

$ fw ls
admin neuroscience
admin clinical
admin psychology

Use ls again to show projects and sessions. For sessions, one can see the timestamp and subject code. In the example below, the last entry is an attachment on the project.

$ fw ls neuroscience
admin Amygdala Structure
admin Cerebellum Circuitry
$ fw ls "neuroscience/Cerebellum Circuitry"
admin May  7 08:42 ccirc_sub_1   ccirc_sub_1_ccirc_ses2_protB
admin Jan  7 17:30 ccirc_sub_1   ccirc_sub_1_ccirc_ses1_protA
# ...
admin Jun 14 16:52               InformedConsent_MRI.pdf

Note: Double quotes are required when there are spaces in the pathname.

Learn More About Using the Flywheel CLI

The following articles explain how to use the Flywheel CLI for common tasks: