Welcome to the new and improved Flywheel Documentation Portal! Please let us know how we're doing. Provide Feedback.
logo
Flywheel Documentation
Index
Initializing search
    • Home
    • User Guides
    • Clinical
    • Data Transfer
    • CLI
    • Developer
    • Administration
    • Release Notes
    • Forum
    • Support
    • Index
    • Home
    • User Guides
        • How to Replace Legacy API Keys
        • Using University Credentials to Sign In
        • The Flywheel hierarchy
        • Project Tab
        • Subject Tab
        • Session Tab
        • Acquisitions
        • File Versioning
        • Timestamps
        • Filtering Data
        • Selecting Data In Flywheel
        • Provenance Tab
        • Subject View
        • Creating and Using Collections
        • Moving a Session to a Different Project
        • Moving An Acquisition
        • Moving Sessions
        • Smart Copy
        • Adding Attachments
        • Data Exchange
        • De-Identification Overview
        • Discovery Dashboard Quick Start
        • File Types in Flywheel
        • Finding Uploaded Data
        • Illegal Characters
        • Creating Custom Forms with Form Builder
        • Installation of Form Builder and Viewer
        • Finding Data in Flywheel
        • Search
        • Basic Search
        • Advanced Search
        • Searching Custom Metadata Fields
        • Site Wide Project Catalog
        • BrainBrowser Info
        • Introduction to Read Tasks
        • Minimum Required DICOM Tags for Functionality
          • Minimum Required DICOM Tags
          • OHIF Config File
          • Supported SOP Class UID Values
          • Viewer Indexing Errors
          • View and Annotate Images
          • Annotate Images
          • 3D segmentations
          • TMTV Mode
          • View Images
        • Study Participant Project Report
          • Data Views
          • Data Views Available Fields and Technical Specifications
        • Add and Edit Custom Metadata
        • Annotating Data
        • Custom Metadata - Adding/Editing
        • Data Classification
        • Using Custom Project Info to Define Custom Classifications
        • Gears
          • Analysis Tab
          • Analysis Gears
          • Building a MATLAB Gear
          • Dcm2niix Troubleshooting
          • Gear Exchange
          • Gear Rule Processing Details
          • Gear Rules
          • Types of Gears
          • Gear Type and Gear Access
          • Introduction to a SDK Gear
          • Obtaining an Error File when Debugging fMRIPrep Failures
          • Prioritizing Jobs and Gear Execution
          • Running a Flywheel Job Locally with Docker
          • Running an Analysis Gear on a Subject
          • Running Gears as a Batch
          • Tag Management
          • Using the Jobs Log, Views, Tabs and Actions
          • Utility Gears
            • Automated Quality Assurance: MRIQC Gear
            • Best Practices: Naming Acquisitions for Automated Classification
            • Gear Versioning
            • Use Gear Rules to Automate Data Preprocessing
            • Including a FreeSurfer License File to Run a FreeSurfer or fMRIPrep Gear
          • Flywheel Notebooks User Guide
        • Downloaded Files with .MISSING Extension
        • Downloading a File from the Web UI
        • Downloading an Entire Project from the Web UI
        • Downloading Analysis Outputs Using the Flywheel UI and SDK
        • Downloading Sessions or Acquisitions from Web UI
        • Unzipping dcm.zip in a Downloaded Flywheel Project
        • Deleting Data
        • Deleting Flywheel Data
          • OHBM 2020: Automating BIDS Workflow with Flywheel
          • Customer Success Story
          • Export a Project in BIDS Format
          • Flywheel + BIDS: Getting Started
          • Importing Existing BIDS Data
          • Storing BIDS Sidecars
          • BIDS Study Design Spreadsheet
          • Webinar: BIDS Templating
          • Viewing BIDS Metadata in Flywheel
          • Ignoring Certain Images in Bids
        • Validated Instance
          • Validated Instance - Audit Trail
          • Validated Instance - Delete Reason
          • Validated Instance - MFA Digital Signature
          • Validated Instance - Project Locking
    • Clinical
        • Annotating Data
        • Revert to the Legacy DICOM/NIfTI Viewer
        • Creating a Viewer Protocol
        • OHBM 2020: Automating BIDS Workflow with Flywheel
        • OHBM 2020: Data Curation and Machine Learning Presentation
        • OHBM 2020: Open Science, Reuse, and Reproducibility
      • Grant Resources
      • Getting Data In
        • Ad hoc Upload
        • Bulk Import
          • How to Import Data (Web App)
          • How to Import Data (CLI)
          • Monitoring
          • Cancelling
          • Troubleshooting
            • Conflict Handling
            • De-Identification
            • Malware Scanning
            • Mapping Rules (19.4+)
            • Mapping Rules (19.2-19.3)
            • Mapping Rules (-19.1)
            • Reference-in-Place
        • DICOM Connector
          • Capturing Data Directly from MR Scanner
          • Naming Acquisitions for Automated Classification
          • Import Flywheel Data from a DIMSE Peer Application
        • (Legacy) DICOM Upload
          • Detect Duplicate Files with Ingest (Legacy)
          • Ingest Template - Parameters Reference
          • Step 1: Create a Template for File Upload
          • Step 2: De-identify Data
          • Step 3: Adding Additional Settings
          • Step 4: Run the Command
      • Getting Data Out
        • Bulk Export
        • Migrating Project Data between Flywheel Sites
    • CLI
        • Installation
        • Updating
        • Configuration File
        • Usage and Examples
        • fw deid
        • fw download
        • fw export bids
        • fw ingest
          • Bids
          • Dicom
            • Importing DICOM Files Using the Flywheel CLI
          • Folder
            • Importing a Structured Folder of Imaging Data with the CLI
          • Project
          • Template
            • Template Overview
            • Template Reference Guide
            • How To Create a Template
            • Template Examples
            • De-identify Data with Ingest
            • Audit Log
            • Detect Duplicates
            • Cluster Ingest
            • AWS S3 Credentials
            • Detecting Duplicate Files with fw ingest
        • fw ls
        • fw sync
          • Export Templates
        • fw upload
        • Finding Logs
        • Temporary Storage Location
        • Login Issues
        • Startup Error
        • Support for MacOS 10.15 Catalina
        • Flywheel CLI Login Issues
    • Developer
      • SDK and API
      • Gear
        • Specifications
        • Building Tutorial
          • Part 1 - Developing Gears
          • Part 2 - Creating Your First Gear
          • Part 3 - The Flywheel Environment
          • Part 4 - The Run Script
          • Part 5 - The Manifest
          • Part 6 - The Dockerfile
          • Part 7 - Running a Gear Locally
          • Part 8 - Logging
          • Part 9 - Debugging
        • Gear Exchange
        • Gear Permissions
        • Gear Rules with SDK Gears
        • Gear Toolkit
      • UI Extension App
      • BIDS
          • Part 1 - Preparing Data
          • Part 2 - Relabeling
          • Part 3 - Running the BIDS Curation Gear
          • Part 4 - Interpreting the Curation Report
          • Part 5 - Field Maps and IntendedFors
          • Part 6 - Extending the Curation Template
        • Differences Between the Flywheel and BIDS Hierarchy
        • How the BIDS Template Engine Processes Data
        • The BIDS Template File
        • Gearify the BIDS app template
        • Update a BIDS app gear
      • Toolkit
        • fw-client
        • fw-file
        • fw-gear
        • fw-classification
      • Webinar Series
        • Webinar Series: Intro to the Flywheel SDK
        • Flywheel Webinar: FlyQL and Advanced Searching in the SDK
        • Webinar Series: Flywheel SDK to Create Containers
        • Webinar Series: Finding Material with Python SDK
        • Webinar Series: Intro to Flywheel Gear Building
    • Administration
        • Add Users
        • Delete Users
        • Roles & Permissions Overview
        • Create Custom Roles
        • Access Logs
        • Manage Site Mode
        • Adding Institutional Collaborators
        • ORCID Account Configuration
        • Troubleshooting Authentication
        • Overview
        • Creating API Keys
      • Data Backup
      • De-Identification
        • Create a De-ID Profile
        • De-ID Profile Transformation Reference Guide
        • De-Identification Profiles
        • Enable a De-ID Profile for a Project, Group, or Site
        • How to De-identify DICOM Files Using the DICOM Uploader
        • How to De-identify Private DICOM Tags
        • Create a De-ID Profile
        • De-Identify DICOM Files Using the CLI
      • Devices
        • Devices Overview
        • Managing Devices
        • API Access Controls for Devices
      • External Storages
        • How-To Configure a Storage
        • Pre-Configured Credentials
      • Extension Applications
        • Gear Menu Organization
        • Gear Rule Templates
        • Setting Gear Access Permissions
        • Delete Gears
        • Software and Computing Requirements for HPC Client System
        • Using Pre-built Singularity Images (.sif) with HPC
        • Create a Group and Project
        • Create a Project
        • Project Template
        • Session Templates
        • Site Shared Data Views
        • Site Bookmarks
        • What is the Unknown Group and Unsorted Project?
        • Discovery Control Panel User Guide
        • Discovery Control Panel Configuration
        • Discovery to Core Data Export
        • Usage Report
    • Release Notes
        • Deprecation of Legacy API Keys
        • Gear Outputs Limited to 100 Files
        • Deprecation of 'fw import' Command (CLI)
        • Change to Flywheel Generated CSV and TSV files
        • Deprecation of Analysis Inputs Filename APIs
        • Removal of the BrainBrowser and EEG Viewers
        • Deprecation of Legacy Viewer
        • Removal of the Montage Viewers
        • Deprecation of regenerate_key commands
        • Deprecation of "Upload DICOM" Feature
        • Removal of Gravatar Integration
        • Flywheel Core 20.3
        • Flywheel Core 20.2
        • Flywheel Core 20.1
        • Flywheel Core 20.0
        • Flywheel Core 19.5
        • Flywheel Core 19.4
        • Flywheel Core 19.3
        • Flywheel Core 19.2
        • Flywheel Core 19.1
        • Flywheel Core 19.0
        • Flywheel Core 18.5
        • Flywheel Core 18.4
        • Flywheel Core 18.3
        • Flywheel Core 18.2
        • Flywheel Core 18.1
        • Flywheel Core 18.0
        • Flywheel Core 17.x
        • Flywheel Core 16.x
        • Flywheel Core 15.x
        • Flywheel Core 14.x
    • Forum
    • Support
      • Find your Flywheel Version
      • Viewing Your Support Tickets
        • Unable to Sign In
        • How to Request changes in JupyterLab compute options
        • How to Request Gear GPU Compute
        • How to Request Gear Compute Changes
        • Determining the Available GPU Drivers
        • Compute Troubleshooting based on Gear Logs
        • Unable to Create an Unsorted Project
    • Index

    Index

    Forum

    We're redirecting you our forums. If this doesn't happen automatically please click this link.

    November 14, 2024 March 27, 2024
    Copyright © 2024 Flywheel. All Rights Reserved

    Cookie Consent

    This website uses cookies to improve your experience on this website and across the web. For more detail about the information we share about your use of our site with our advertising and analytics partners, see our Privacy Policy