Tags

Following is a list of relevant tags:

API

• Overview
• Creating API Keys

Access

• Add Users
• Create Custom Roles
• Setting Gear Access
• Adding Institutional Collaborators
• ORCID Account Configuration

Adding Data

• Getting Data In

Admin

• Gear Permissions
• Access Logs
• Add Users
• Create Custom Roles
• Delete Users
• Manage Site Mode
• Roles & Permissions Overview
• Overview
• Creating API Keys
• Backing up Data
• Delete Gears
• Gear Menu Organization
• Gear Rule Templates
• Setting Gear Access
• Setting Gear Access Permissions
• Software and Computing Requirements for HPC Client System
• Using Pre-built Singularity Images (.sif) with HPC
• 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
• Interfaces - Devices, DICOM Peers, External Storage
• Devices Overview
• Managing Devices
• Discovery Control Panel User Guide
• Discovery Control Panel Configuration
• Extension Applications Setup
• Overview
• Pre-Configured Credentials
• How-To Configure a Storage
• Create a Group and Project
• Create a Project
• Site Shared Data Views
• Project Template
• Session Templates
• Site Bookmarks
• What is the Unknown Group and Unsorted Project?
• Adding Institutional Collaborators
• Troubleshooting Authentication
• ORCID Account Configuration

Annotate

• View and Annotate Images

Audit

• Audit Log
• Troubleshooting

Audit Trail

• Validated Instance - Audit Trail

Auditing

• Access Logs

Authentication

• Using University Credentials to Sign In

Azure ML

• Flywheel Azure ML Integration

BIDS

• The fw export bids Command
• Ingesting Data in BIDS Format using the CLI
• 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
• Export a Project in BIDS Format
• Flywheel + BIDS: Getting Started
• Importing Existing BIDS Data
• BIDS Study Design Spreadsheet
• Webinar: BIDS Templating
• Ignoring Certain Images in Bids

BIDS App template

• Gearify the BIDS app template

Browse

• The fw ls Command

CLI

• The Flywheel Command-Line Interface (CLI)
• The fw deid Command
• The fw download Command
• The fw export bids Command
• The fw ingest Command
• Detecting Duplicate Files with fw ingest
• Audit Log
• Cluster Ingest
• AWS S3 Credentials
• Importing a Structured Folder of Imaging Data with the CLI
• Using the fw ingest template Command
• Template Examples
• Template Overview
• How To Create a Template
• De-identify Data with Ingest
• Template Reference Guide
• The fw ls Command
• The fw sync Command
• Export Templates
• The fw upload Command
• Configuration File
• Usage and Examples
• Installation
• Updating
• Finding Logs
• Flywheel CLI Login Issues
• Startup Error
• Temporary Storage Location
• Support for MacOS 10.15 Catalina

Clinical

• Grant Resources
• OHBM 2020: Automating BIDS Workflow with Flywheel
• OHBM 2020: Data Curation and Machine Learning Presentation
• OHBM 2020: Open Science, Reuse, and Reproducibility
• Creating a Viewer Protocol
• Annotating Data
• Revert to the Legacy DICOM/NIfTI Viewer
• OHBM 2020: Automating BIDS Workflow with Flywheel
• Minimum Required DICOM Tags
• Supported SOP Class UID Values
• Viewer Indexing Errors
• View and Annotate Images

Clinical Guide

• Creating a Viewer Protocol

Conflict Handling

• Conflict Handling

Connector

• Getting Data In
• How the DICOM Connector Uploads an Image
• Capturing Data Directly from MR Scanner
• Naming Acquisitions for Automated Classification
• Capturing Data Directly from MR Scanner
• How the DICOM Connector Uploads an Image
• Import Flywheel Data from a DIMSE Peer Application

Data Views

• Data Views Available Fields and Technical Specifications

De-ID Profile

• The fw deid Command
• De-Identification Overview
• 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 Private DICOM Tags
• Create a De-ID Profile

De-identification

• The fw deid Command
• De-identify Data with Ingest
• De-Identification Overview
• 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
• De-Identification
• Step 2: De-identify Data
• De-Identification Overview

Delete Reason

• Validated Instance - Delete Reason

Dev

• Update a BIDS app gear

Dev Guide

• 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
• Extension Applications

Developer

• 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
• Webinar Series Intro to Flywheel Gear Building
• Webinar Series Intro to the Flywheel SDK

Developer Guide

• Update a BIDS app gear

Devices

• Interfaces - Devices, DICOM Peers, External Storage
• Devices Overview
• Managing Devices

Digital Signature

• Validated Instance - MFA Digital Signature
• Validated Instance - Project Locking

Discovery

• Discovery Control Panel Configuration
• Discovery to Core Data Export
• Discovery Dashboard Quick Start

Download

• The fw download Command
• Downloading Data
• 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

Duplicate Handling

• Detecting Duplicate Files with fw ingest
• Conflict Handling
• Detect Duplicate Files with Ingest (Legacy)

Example

• Template Examples
• Usage and Examples
• 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

Export

• The fw export bids Command
• Downloading Data
• Bulk Exports
• 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

External Storage

• Interfaces - Devices, DICOM Peers, External Storage
• Overview
• Pre-Configured Credentials
• How-To Configure a Storage

GPU

• Determining the Available GPU Drivers

Gear Rules

• Gear Rule Processing Details
• Gear Rules
• Prioritizing Jobs and Gear Execution
• Use Gear Rules to Automate Data Preprocessing

Gears

• 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
• 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
• Webinar Series Intro to Flywheel Gear Building
• Gear Menu Organization
• Gear Rule Templates
• Setting Gear Access
• Setting Gear Access Permissions
• Delete Gears
• Determining the Available GPU Drivers
• Flywheel Gears
• Analysis Gears
• Dcm2niix Troubleshooting
• Gear Exchange
• Gear Rules
• Types of Gears
• Gear Type and Gear Access
• Introduction to a SDK Gear
• 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
• Gear Versioning
• Use Gear Rules to Automate Data Preprocessing
• Including a FreeSurfer License File to Run a FreeSurfer or fMRIPrep Gear
• Using Custom Project Info to Define Custom Classifications
• Provenance Tab

Getting Started

• Usage and Examples
• Installation
• Updating
• 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
• Add Users
• Create a Group and Project
• Create a Project
• Create a Group and Project
• Create a Project
• Adding Institutional Collaborators
• Troubleshooting Authentication
• ORCID Account Configuration
• Welcome to Flywheel
• Flywheel + BIDS: Getting Started
• De-Identification Overview
• Webinar Series Intro to Flywheel

How To

• How To Create a Template
• De-identify Data with Ingest
• Installation
• How to Import Data (CLI)
• How to Import Data (Web App)
• Step 1: Create a Template for File Upload
• Step 2: De-identify Data
• Step 3: Adding Additional Settings
• Step 4: Run the Command
• Bulk Exports
• Moving a Session to a Different Project

Images

• View and Annotate Images

Import

• Getting Data In
• Bulk Import
• Cancelling
• Conflict Handling
• How to Import Data (CLI)
• How to Import Data (Web App)
• Mapping Rules (-19.1)
• Mapping Rules (19.2+)
• Monitoring
• Reference-in-Place
• Troubleshooting
• De-Identification

Import by Reference

• Reference-in-Place

Ingest

• The fw ingest Command
• Detecting Duplicate Files with fw ingest
• Audit Log
• Cluster Ingest
• AWS S3 Credentials
• Importing a Structured Folder of Imaging Data with the CLI
• Using the fw ingest template Command
• Template Examples
• Template Overview
• How To Create a Template
• De-identify Data with Ingest
• Template Reference Guide
• 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

Ingest Folder

• Importing a Structured Folder of Imaging Data with the CLI

Ingest Template

• Using the fw ingest template Command
• Template Examples
• Template Overview
• How To Create a Template
• De-identify Data with Ingest
• Template Reference Guide
• 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

Install

• Installation

Integrations

• Flywheel Azure ML Integration

MFA

• Validated Instance - MFA Digital Signature

Machine Learning

• Flywheel Azure ML Integration

Mapping

• Mapping Rules (-19.1)
• Mapping Rules (19.2+)

Metadata

• Custom Metadata - Adding/Editing

Moving Acquisitions

• Moving An Acquisition

Moving Sessions

• Moving a Session to a Different Project
• Moving Sessions

Navigation

• The fw ls Command

Notebooks

• Determining the Available GPU Drivers

Overview

• The Flywheel Command-Line Interface (CLI)
• The fw ingest Command
• Getting Data In
• Bulk Import
• Downloading Data
• Bulk Exports
• Validated Instance - Overview

Project Locking

• Validated Instance - Project Locking

Reaper

• How the DICOM Connector Uploads an Image
• Capturing Data Directly from MR Scanner
• Naming Acquisitions for Automated Classification
• Capturing Data Directly from MR Scanner
• How the DICOM Connector Uploads an Image
• Import Flywheel Data from a DIMSE Peer Application

Reference

• The fw deid Command
• The fw download Command
• The fw export bids Command
• The fw ingest Command
• Audit Log
• Cluster Ingest
• AWS S3 Credentials
• Using the fw ingest template Command
• Template Overview
• Template Reference Guide
• The fw ls Command
• The fw sync Command
• Export Templates
• The fw upload Command
• Ingest Template - Parameters Reference
• Bulk Exports

Reference-in-place

• Reference-in-Place

S3

• AWS S3 Credentials

SDK

• Flywheel Webinar FlyQL and Advanced Searching in the SDK
• Webinar Series Finding Material with Python SDK
• Webinar Series Flywheel SDK to Create
• Webinar Series Intro to the Flywheel SDK
• Introduction to a SDK Gear
• Downloading Analysis Outputs Using the Flywheel UI and SDK

Search

• Basic Search
• Search
• Searching Custom Metadata Fields
• Flywheel Webinar FlyQL and Advanced Searching in the SDK

Site Admin

• Gear Permissions
• Access Logs
• Add Users
• Create Custom Roles
• Delete Users
• Manage Site Mode
• Roles & Permissions Overview
• Overview
• Creating API Keys
• Backing up Data
• Delete Gears
• Gear Menu Organization
• Gear Rule Templates
• Setting Gear Access Permissions
• Software and Computing Requirements for HPC Client System
• Using Pre-built Singularity Images (.sif) with HPC
• Devices Overview
• Managing Devices
• Discovery Control Panel User Guide
• Discovery Control Panel Configuration
• Extension Applications Setup
• Overview
• Pre-Configured Credentials
• How-To Configure a Storage
• Create a Group and Project
• Create a Project
• Site Shared Data Views
• Project Template
• Session Templates
• Site Bookmarks
• What is the Unknown Group and Unsorted Project?
• Adding Institutional Collaborators
• Troubleshooting Authentication
• ORCID Account Configuration

Smart Copy

• Smart Copy

Sync

• The fw sync Command
• Export Templates
• Downloading Data

Timestamps

• Timestamps

Troubleshooting

• Finding Logs
• Flywheel CLI Login Issues
• Startup Error
• Temporary Storage Location
• Support for MacOS 10.15 Catalina
• Troubleshooting
• Unable to Sign In
• How to Request Gear Compute Changes
• Determining the Available GPU Drivers
• How to Request Gear GPU Compute
• How to Request changes in JupyterLab compute options
• Unable to Create an Unsorted Project
• Dcm2niix Troubleshooting
• Viewer Indexing Errors

Tutorial

• 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

Update

• Updating

Upload

• The fw upload Command
• Getting Data In
• Ad hoc Upload
• (Legacy) DICOM Upload
• How to Import Data (Web App)
• De-Identification

User

• Gearify the BIDS app template
• Storing BIDS Sidecars

User Guide

• Gearify the BIDS app template
• Delete Gears
• Flywheel HPC-Client: Minimum software and computing requirements
• Discovery to Core Data Export
• Create a Group and Project
• Create a Project
• Site Bookmarks
• Find your Flywheel Version
• Viewing Your Support Tickets
• 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
• Flywheel Azure ML Integration
• Flywheel Notebooks User Guide
• Flywheel 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
• Deleting Data
• Deleting Flywheel Data
• 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
• Add and Edit Custom Metadata
• Annotating Data
• Custom Metadata - Adding/Editing
• Data Classification
• Using Custom Project Info to Define Custom Classifications
• Creating Custom Forms with Form Builder
• Installation of Form Builder and Viewer
• Acquisitions
• File Versioning
• Filtering Data
• Project Tab
• Provenance Tab
• Selecting Data In Flywheel
• Session Tab
• Subject Tab
• Subject View
• Timestamps
• Creating and Using Collections
• Moving a Session to a Different Project
• Moving An Acquisition
• Moving Sessions
• Smart Copy
• Study Participant Project Report
• Data Views
• Data Views Available Fields and Technical Specifications
• Advanced Search
• Basic Search
• Finding Data in Flywheel
• Search
• Searching Custom Metadata Fields
• Site Wide Project Catalog
• Using University Credentials to Sign In
• Adding Attachments
• Data Exchange
• De-Identification Overview
• Discovery Dashboard Quick Start
• File Types in Flywheel
• Validated Instance - Audit Trail
• Validated Instance - Delete Reason
• Validated Instance - MFA Digital Signature
• Validated Instance - Project Locking
• BrainBrowser Info
• Introduction to Read Tasks
• Minimum Required DICOM Tags for Functionality
• Flywheel Webinar FlyQL and Advanced Searching in the SDK
• Webinar Series Intro to Flywheel
• Webinars

User Guides

• Validated Instance - Overview

Users

• Add Users
• Create Custom Roles
• Adding Institutional Collaborators
• Troubleshooting Authentication
• ORCID Account Configuration

Validated Instance

• Validated Instance - Overview
• Validated Instance - Audit Trail
• Validated Instance - Delete Reason
• Validated Instance - MFA Digital Signature
• Validated Instance - Project Locking

Viewer

• Supported SOP Class UID Values
• Viewer Indexing Errors

Viewer Protocol

• Creating a Viewer Protocol

Webinar

• Webinar Series Finding Material with Python SDK
• Webinar Series Flywheel SDK to Create
• Webinar Series Intro to Flywheel Gear Building
• Webinar Series Intro to the Flywheel SDK
• Webinar: BIDS Templating
• Webinar Series Intro to Flywheel
• Webinars

fw deid

• The fw deid Command
• De-Identify DICOM Files Using the CLI

fw download

• The fw download Command

fw export bids

• The fw export bids Command

fw ls

• The fw ls Command

fw sync

• The fw sync Command

fw upload

• The fw upload Command