Command-Line Interface (CLI) Guides

Getting Started

• Command Line Interface Overview
• Installing the Flywheel Command Line Interface (CLI)
• Update the Flywheel CLI
• CLI Usage and Examples
• The CLI Config File
• Webinar Series: Importing Data With Flywheel's CLI Tools
• Webinar Series: Introduction to the Flywheel CLI

Putting Data In

Upload

• Uploading Individual Files

Ingest

• Ingest BIDS
• Ingest DICOM
• Ingest Folder
• Ingest Project (Copy a Project)
• Ingest Template
  • Creating a Configuration File for Flywheel Ingest
  • Creating a Template File for Flywheel Ingest
  • Include Exclude Settings

Getting Data Out

Download

• Downloading Data With the CLI

Export

• Export BIDS

Sync

• Use the Sync Command for Downloading Data

Additional Functions

Browsing (ls)

• Finding Permissions for Groups and Navigate Flywheel Hierarchy
• Navigating the Flywheel Hierarchy Using CLI

De-Identification (deid)

• Configure De-Identification using a De-ID Profile
• Run the Command to De-identify Data

Troubleshooting

• Locating the CLI Logs
• CLI Temporary Storage Location
• Known Issues
  • CLI Startup Error
  • Troubleshooting CLI Login Issues
  • Running CLI After Updating to MacOS 10.15 Catalina

Deprecated Functions

Import

• CLI Reference Guide: Import Bruker Data
  • Importing Bruker Data
• CLI Reference Guide: Import DICOM
  • Importing DICOM Files Using the Flywheel CLI
• CLI Reference Guide: Import Folder
  • Importing a Structured Folder of Imaging Data
• CLI Reference Guide: Import Par Rec Files
  • Import Par Rec Files
• CLI Reference Guide Import Template