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    • User Guides
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    • 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
    • Developer Guides
      • Gearify the BIDS app template
      • BIDS Curation Tutorial Part 1: Preparing Data
      • BIDS Curation Tutorial Part 2: Running Relabeling
      • BIDS Curation Tutorial Part 3 Running BIDS Curation
      • BIDS Curation Tutorial Part 4 Curation Reports
      • BIDS Curation Tutorial Part 4 Curation Reports
      • BIDS Curation Tutorial Part 5 Fieldmaps and IntendedFor
      • BIDS Curation Tutorial Part 6 Project Curation Template
      • BIDS Curation Tutorial Part 5 Fieldmaps and IntendedFor
      • Differences Between the Flywheel and BIDS Hierarchy
      • How the BIDS Template Engine Processes Data
      • The BIDS Template File
      • Update a BIDS app gear
      • Extension Applications
      • Flywheel Webinar FlyQL and Advanced Searching in the SDK
      • Gear Building Tutorial
      • Gear Building Tutorial Part 1 Developing Gears
      • Gear Building Tutorial Part 2 Creating Your First Gear
      • Gear Building Tutorial Part 3 The Flywheel Environment
      • Gear Building Tutorial Part 4 The Run Script
      • Gear Building Tutorial Part 5: The Manifest
      • Gear Building Tutorial Part 6 The Dockerfile
      • Gear Building Tutorial Part 7: Running a Gear Locally
      • Gear Building Tutorial Part 8 Logging
      • Gear Building Tutorial Part 9 Debugging
      • Gear Exchange
      • Gear Permissions
      • Gear Rules with SDK Gears
      • Gear Specification
      • Gear Versioning
      • Introduction to an SDK Gear
      • Obtaining the Error File When Debugging fMRIPrep Failures
      • Webinar Series Finding Material with Python SDK
      • Webinar Series: Flywheel SDK to Create Containers
      • Webinar Series Intro to Flywheel Gear Building
      • Webinar Series Intro to the Flywheel SDK
      • 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
    • 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
        • Deprecation of regenerate_key commands
        • Deprecation of "Upload DICOM" Feature
        • Removal of Gravatar Integration
        • 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

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    April 29, 2025 December 14, 2023
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