Tags

Following is a list of relevant tags:

API

• Creating API Keys
• Overview

Access

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

Adding Data

• Getting Data In

Admin

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

Admin Guide

• Usage Report

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

BIDS

• 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 5 Fieldmaps and IntendedFor
• BIDS Curation Tutorial Part 6 Project Curation Template
• BIDS Study Design Spreadsheet
• Differences Between the Flywheel and BIDS Hierarchy
• Export a Project in BIDS Format
• Flywheel + BIDS: Getting Started
• Gearify the BIDS app template
• How the BIDS Template Engine Processes Data
• Ignoring Certain Images in Bids
• Importing Existing BIDS Data
• Ingesting Data in BIDS Format using the CLI
• The BIDS Template File
• The fw export bids Command
• Update a BIDS app gear
• Webinar: BIDS Templating

BIDS App template

• Gearify the BIDS app template

Browse

• The fw ls Command

CLI

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

Clinical

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

Clinical Guide

• Creating a Viewer Protocol

Conflict Handling

• Conflict Handling

Connector

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

Data Views

• Data Views Available Fields and Technical Specifications

De-ID Profile

• Create a De-ID Profile
• Create a De-ID Profile
• De-ID Profile Transformation Reference Guide
• De-Identification Overview
• De-Identification Profiles
• Enable a De-ID Profile for a Project, Group, or Site
• How to De-identify Private DICOM Tags
• The fw deid Command

De-identification

• Create a De-ID Profile
• Create a De-ID Profile
• De-ID Profile Transformation Reference Guide
• De-Identification
• De-Identification Overview
• De-Identification Overview
• De-Identification Profiles
• De-Identify DICOM Files Using the CLI
• De-identify Data with Ingest
• 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
• Step 2: De-identify Data
• The fw deid Command

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 5 Fieldmaps and IntendedFor
• BIDS Curation Tutorial Part 6 Project Curation Template
• Differences Between the Flywheel and BIDS Hierarchy
• Extension Applications
• How the BIDS Template Engine Processes Data
• The BIDS Template File

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 Intro to Flywheel Gear Building
• Webinar Series Intro to the Flywheel SDK
• Webinar Series: Flywheel SDK to Create Containers

Developer Guide

• Update a BIDS app gear

Devices

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

Digital Signature

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

Discovery

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

Download

• Downloaded Files with .MISSING Extension
• Downloading Analysis Outputs Using the Flywheel UI and SDK
• Downloading Data
• Downloading Sessions or Acquisitions from Web UI
• Downloading a File from the Web UI
• Downloading an Entire Project from the Web UI
• The fw download Command

Duplicate Handling

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

Example

• 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
• Template Examples
• Usage and Examples

Export

• Bulk Exports
• Downloaded Files with .MISSING Extension
• Downloading Analysis Outputs Using the Flywheel UI and SDK
• Downloading Data
• Downloading Sessions or Acquisitions from Web UI
• Downloading a File from the Web UI
• Downloading an Entire Project from the Web UI
• The fw export bids Command

External Storage

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

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

• Analysis Gears
• Automated Quality Assurance: MRIQC Gear
• 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 5 Fieldmaps and IntendedFor
• BIDS Curation Tutorial Part 6 Project Curation Template
• Compute Troubleshooting based on Gear Logs
• Dcm2niix Troubleshooting
• Delete Gears
• Determining the Available GPU Drivers
• Flywheel Gears
• 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 Exchange
• Gear Menu Organization
• Gear Permissions
• Gear Rule Templates
• Gear Rules
• Gear Rules with SDK Gears
• Gear Specification
• Gear Type and Gear Access
• Gear Versioning
• Gear Versioning
• Including a FreeSurfer License File to Run a FreeSurfer or fMRIPrep Gear
• Introduction to a SDK Gear
• Introduction to an SDK Gear
• Prioritizing Jobs and Gear Execution
• Provenance Tab
• Running Gears as a Batch
• Running a Flywheel Job Locally with Docker
• Running an Analysis Gear on a Subject
• Setting Gear Access
• Setting Gear Access Permissions
• Tag Management
• Types of Gears
• Use Gear Rules to Automate Data Preprocessing
• Using Custom Project Info to Define Custom Classifications
• Using the Jobs Log, Views, Tabs and Actions
• Utility Gears
• Webinar Series Intro to Flywheel Gear Building

Getting Started

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

How To

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

Images

• View and Annotate Images

Import

• Bulk Import
• Cancelling
• Conflict Handling
• De-Identification
• Getting Data In
• How to Import Data (CLI)
• How to Import Data (Web App)
• Malware Scanning
• Mapping Rules (-19.1)
• Mapping Rules (19.2-19.3)
• Mapping Rules (19.4+)
• Monitoring
• Reference-in-Place
• Troubleshooting

Import by Reference

• Reference-in-Place

Ingest

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

Ingest Folder

• Importing a Structured Folder of Imaging Data with the CLI

Ingest Template

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

Install

• Installation

Jobs

• Compute Troubleshooting based on Gear Logs

MFA

• Validated Instance - MFA Digital Signature

Malware Scanning

• Malware Scanning

Mapping

• Mapping Rules (-19.1)
• Mapping Rules (19.2-19.3)
• Mapping Rules (19.4+)

Metadata

• Custom Metadata - Adding/Editing

Moving Acquisitions

• Moving An Acquisition

Moving Sessions

• Moving Sessions
• Moving a Session to a Different Project

Navigation

• The fw ls Command

Notebooks

• Determining the Available GPU Drivers

Overview

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

Project Locking

• Validated Instance - Project Locking

Reaper

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

Reference

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

Reference-in-place

• Reference-in-Place

S3

• AWS S3 Credentials

SDK

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

Search

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

Site Admin

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

Site Usage Report

• Usage Report

Smart Copy

• Smart Copy

Sync

• Downloading Data
• Export Templates
• The fw sync Command

Timestamps

• Timestamps

Troubleshooting

• Compute Troubleshooting based on Gear Logs
• Dcm2niix Troubleshooting
• Determining the Available GPU Drivers
• Finding Logs
• Flywheel CLI Login Issues
• How to Request Gear Compute Changes
• How to Request Gear GPU Compute
• How to Request changes in JupyterLab compute options
• Startup Error
• Support for MacOS 10.15 Catalina
• Temporary Storage Location
• Troubleshooting
• Unable to Create an Unsorted Project
• Unable to Sign In
• 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 5 Fieldmaps and IntendedFor
• BIDS Curation Tutorial Part 6 Project Curation Template

Update

• Updating

Upload

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

Usage Report

• Usage Report

User

• Gearify the BIDS app template
• Storing BIDS Sidecars

User Guide

• Acquisitions
• Add and Edit Custom Metadata
• Adding Attachments
• Advanced Search
• Analysis Gears
• Analysis Tab
• Annotating Data
• Automated Quality Assurance: MRIQC Gear
• BIDS Study Design Spreadsheet
• Basic Search
• Best Practices: Naming Acquisitions for Automated Classification
• BrainBrowser Info
• Building a MATLAB Gear
• Create a Group and Project
• Create a Project
• Creating Custom Forms with Form Builder
• Creating and Using Collections
• Custom Metadata - Adding/Editing
• Customer Success Story
• Data Classification
• Data Exchange
• Data Views
• Data Views Available Fields and Technical Specifications
• Dcm2niix Troubleshooting
• De-Identification Overview
• Delete Gears
• Deleting Data
• Deleting Flywheel Data
• Discovery Dashboard Quick Start
• Discovery to Core Data Export
• Downloaded Files with .MISSING Extension
• Downloading Analysis Outputs Using the Flywheel UI and SDK
• Downloading Sessions or Acquisitions from Web UI
• Downloading a File from the Web UI
• Downloading an Entire Project from the Web UI
• Export a Project in BIDS Format
• File Types in Flywheel
• File Versioning
• Filtering Data
• Find your Flywheel Version
• Finding Data in Flywheel
• Flywheel + BIDS: Getting Started
• Flywheel Gears
• Flywheel HPC-Client: Minimum software and computing requirements
• Flywheel Notebooks User Guide
• Flywheel Webinar FlyQL and Advanced Searching in the SDK
• Gear Exchange
• Gear Rule Processing Details
• Gear Rules
• Gear Type and Gear Access
• Gear Versioning
• Gearify the BIDS app template
• Ignoring Certain Images in Bids
• Importing Existing BIDS Data
• Including a FreeSurfer License File to Run a FreeSurfer or fMRIPrep Gear
• Installation of Form Builder and Viewer
• Introduction to Read Tasks
• Introduction to a SDK Gear
• Minimum Required DICOM Tags for Functionality
• Moving An Acquisition
• Moving Sessions
• Moving a Session to a Different Project
• Obtaining an Error File when Debugging fMRIPrep Failures
• Prioritizing Jobs and Gear Execution
• Project Tab
• Provenance Tab
• Running Gears as a Batch
• Running a Flywheel Job Locally with Docker
• Running an Analysis Gear on a Subject
• Search
• Searching Custom Metadata Fields
• Selecting Data In Flywheel
• Session Tab
• Site Bookmarks
• Site Wide Project Catalog
• Smart Copy
• Storing BIDS Sidecars
• Study Participant Project Report
• Subject Tab
• Subject View
• Tag Management
• Timestamps
• Types of Gears
• Unzipping dcm.zip in a Downloaded Flywheel Project
• Use Gear Rules to Automate Data Preprocessing
• Using Custom Project Info to Define Custom Classifications
• Using University Credentials to Sign In
• Using the Jobs Log, Views, Tabs and Actions
• Utility Gears
• Validated Instance - Audit Trail
• Validated Instance - Delete Reason
• Validated Instance - MFA Digital Signature
• Validated Instance - Project Locking
• Viewing BIDS Metadata in Flywheel
• Viewing Your Support Tickets
• Webinar Series Intro to Flywheel
• Webinar: BIDS Templating
• Webinars

User Guides

• Validated Instance - Overview

Users

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

Validated Instance

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

Viewer

• Supported SOP Class UID Values
• Viewer Indexing Errors

Viewer Protocol

• Creating a Viewer Protocol

Virus Scanning

• Malware Scanning

Webinar

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

fw deid

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

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