Exporting Data in BIDS Format using the CLI
Introduction
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.
Note
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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 also includes 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
Instruction Steps
- Download the Flywheel CLI and sign in to Flywheel.
- Open Terminal or Windows Command Prompt.
- Enter the export bids command:
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
...
- Your data is downloaded to your computer, and your project maintains its BIDS format.
Example:
Reference Guide
Required Flags
| 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 \ | |
| --project \ | Sets the label for the project |
| --subject SUBJECT | Exports data for a single subject (ex. sub-01) |
| --session SESSION | Exports data from a single session (ex. ses-01) |
| --data-type DATA TYPE | Exports only the given data type (ex. 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 |