Exporting a BIDS Project using the CLI

  • Updated

If you have a project that follows the BIDS format, you can use the CLI to download the project so it stays in the BIDS format.

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Before you begin

It is required that your project is already in the BIDS format to use the export bids command. If your project isn't yet in BIDS format, see our resources for help transitioning to BIDS. This includes also running the BIDS curation gear on your project. 

If you data is not in BIDS format, use the fw download command to download files.

Usage

fw export bids [Project in Flywheel] [Destination folder] [optional flags]

Steps

  1. Download the Flywheel CLI, and sign in to Flywheel.

  2. Open Terminal or Windows Command Prompt.

  3. Enter the export bids command:

    $ fw export bids -p "Project Name" [Destination folder]

    for example:

    $ fw export bids -p "Anxiety Study" ~/Documents/FlywheelData
INFO: Verify download directory exists
INFO: Processing project files
INFO: Processing session files
INFO: Processing acquisition files
INFO: Downloading project files
INFO: Downloading session files
INFO: Downloading acquisition files
INFO: Downloading acquisition file: sub-13_inplaneT2.nii.gz
...

  4. Your data is downloaded to your computer, and your project maintains its BIDS format. For example:

    15df166e602118.jpg

Reference Guide

Required

Required argument

Description

-p

--project

The Project label in Flywheel. If the project label includes spaces, make sure to use quotes. For example "My Project"

[dest folder]

The path to the folder on your computer where you want to export the data to

 

Optional Flags

Optional Flag

Description

-h

--help

Displays the help for the command

-c FILE LOCATION

--config-file FILE LOCATION

Uses the config file to set the flags for the command. See our article on how to create and use the config file to set optional flags for commands. 

-y

-yes

Assume the answer is yes to all prompts

--no-config

Do not load the default config file

--ca-certs CERTS

The file to use for SSL Certificate Validation

--timezone TIMEZONE

Sets the timestamp for imports to the local timezone where they were uploaded

--debug

Turns on debug logging

--quiet

Turns off log messages to the console

-p <label>

--project <label>

Sets the label for the project

--subject SUBJECT

Exports data for a single subject (for example sub-01)

--session SESSION

Exports data from a single session (for example ses-01)

--data-type DATA TYPE

Exports only the given data type (for example func). Currently you can only indicate one data type. To include multiple data types, enter this flag more than once. For example:  

fw export bids -p "Anxiety Study" ~/Documents/FlywheelData --data-type func --data-type anat

--source-data

Includes source data