HED Resources
0.0.1

Overview:

  • Introduction to HED
    • Brief history of HED
      • HED generation 1
      • HED generation 2
      • HED generation 3
    • Goals of HED
    • A basic HED annotation
    • How to get started
  • What’s new?
  • How do you use HED?
    • As an experimenter
      • Planning and running an experiment
        • Event acquisition
        • Logs to event files
      • Post-processing the event data
    • As a data annotator
      • Standardizing the format
        • Learning about BIDS
        • Learning about HED
        • Integrating HED in BIDS
      • Adding HED annotations
        • Viewing available tags
        • Basic annotation strategies
        • More advanced annotations
      • Checking correctness
        • Validating HED annotations
        • Checking for consistency
    • As a data analyst
      • Understanding the data
      • Preparing the data
      • Analyzing the data
        • Factor vectors and selection
        • HED analysis in EEGLAB
        • HED support in other tools
    • As a tool developer
      • Integration with existing tools
      • The HED code base
        • The HED python code base
        • The HED JavaScript code base
        • The HED MATLAB code base
        • Web tools and REST services
      • Future development plans
    • As a schema builder
      • Viewing available schemas
      • Improving an existing schema
      • Creating a new library schema
      • Private vocabularies and extensions

Tutorials:

  • BIDS annotation quickstart
    • How HED works in BIDS
      • BIDS event files
      • JSON event sidecars
    • Create a JSON template
      • Step 1: Select generate JSON
      • Step 2: Upload an events file.
      • Step 3: Select columns to annotate
      • Step 4: Download the template.
      • Step 5: Complete the annotation.
    • Spreadsheet templates
      • Step 1: Select extract HED spreadsheet
      • Step 2: Upload a sidecar and extract.
      • Step 3: Edit the spreadsheet
      • Step 4: Merge the spreadsheet
  • HED annotation quickstart
    • What is HED annotation?
    • A recipe for simple annotation
    • Assembly and curly braces
  • Understanding HED versions
    • HED version basics
    • Using HED versions
  • HED annotation in NWB
    • NWB ndx-hed installation
    • NWB ndx-hed examples
      • HedTags as a standalone vector
      • Adding a row to HedTags
      • HED in a table
      • Add a row to a DynamicTable
    • HED and ndx-events
    • HED in NWB files
  • HED validation guide
    • What is HED validation?
    • Types of errors
    • Available validators
      • Python validator
      • JavaScript validator
      • MATLAB support
    • Validation strategies
      • Validation in BIDS
        • Specifying the HED version
        • BIDS online validator
      • HED online validation
      • Validation for MATLAB users
        • Direct access to services
        • Access through EEGLAB
        • Access through Fieldtrip
      • Validation for Python users
        • Jupyter notebooks for validation
        • Remodeling validation summaries
  • HED search guide
    • HED object-based search
      • Object-based search syntax
      • Single tag queries
        • Single-term search
        • Quoted-tag search
        • Tag-path with slash
        • Tag-prefix with wildcard
      • Logical queries
      • Group queries
    • HED text-based search
      • Text-based search syntax
      • Example text-based queries
    • Where can HED search be used?
  • HED summary guide
    • Column value summary
    • HED tag summary
    • Experimental design summary
  • HED conditions and design matrices
    • HED annotations for conditions
      • Direct condition variables
      • Defined condition variables
      • Direct vs defined approaches
      • Column vs row annotations
    • Experimental design concepts
      • Design matrices and factor variables
      • Types of condition encoding
  • HED remodeling quickstart
    • What is remodeling?
    • The remodeling process
    • JSON remodeling files
      • Basic remodel operation syntax
      • Applying multiple remodel operations
      • More complex remodeling
      • Remodeling file locations
    • Using the remodeling tools
      • Online tools for debugging
      • The command-line interface
      • Jupyter notebooks for remodeling
  • HED schema developer’s guide
    • Schema design basics
      • Top-level as categories
      • Is-a
      • Orthogonal design
      • Uniqueness and forms
      • Choosing tag names
      • Design principles for schema
      • Deciding partnership
        • Unpartnered libraries
        • Partnered schemas
        • Why partnership?
      • Naming your schema
    • Creating your schema
      • Introducing MediaWiki
      • Defining a schema
      • Checking syntax
      • Converting to XML
      • Schema versions
      • Schema file names
    • Becoming official
      • Getting listed
      • Proposing changes
      • Releasing a schema
      • Summarizing the process
    • Further documentation

Tool documentation:

  • HED online tools
    • Browser-based access
      • Events files
        • Validate an events file
        • Assemble annotations
        • Search annotations
        • Generate sidecar template
        • Execute remodel script
      • Sidecar files
        • Validate a sidecar
        • Convert sidecar to long
        • Convert sidecar to short
        • Extract spreadsheet from sidecar
        • Merge a spreadsheet with a sidecar
      • Spreadsheet files
        • Validate a spreadsheet
        • Convert spreadsheet to long
        • Convert spreadsheet to short
      • String online tools
        • Validate a HED string
        • Convert a HED string to long
        • Convert HED string to short
      • Schema online tools
        • Validate a HED schema
        • Convert a HED schema
        • Compare HED schemas
    • HED RESTful services
      • Service setup
      • Request format
      • Service responses
  • CTagger GUI tagging tool
    • CTAGGER installation
      • CTAGGER standalone installation
        • Step 1:Check to see that you have Java installed.
        • Step 2: Download CTagger.jar.
        • Step 3: Double-click on CTagger.jar to run.
      • CTAGGER in EEGLAB
    • Loading BIDS event files
    • Adding HED annotation
      • Validating your annotation
  • HED remodeling tools
    • Overview of remodeling
      • Transformation operations
      • Summarization operations
      • Available operations
    • Installing the remodel tools
    • Remodel command-line interface
      • Calling remodel tools
      • Remodel command-line arguments
        • Positional arguments
        • Named arguments
    • Remodel scripts
      • Backing up files
      • Remodeling files
      • Restoring files
    • Remodel with HED
      • Extracting HED information from BIDS
      • Directly specifying HED information
    • Remodel error handling
      • Errors in the remodel file
      • Execution-time remodel errors
    • Remodel sample files
      • Sample remodel file
      • Sample remodel event file
      • Sample remodel sidecar file
    • Remodel transformations
      • Factor column
        • Factor column parameters
        • Factor column example
      • Factor HED tags
        • Factor HED tags parameters
        • Factor HED tags example
      • Factor HED type
        • Factor HED type parameters
        • Factor HED type example
      • Merge consecutive
        • Merge consecutive parameters
        • Merge consecutive example
      • Remap columns
        • Remap columns parameters
        • Remap columns example
      • Remove columns
        • Remove columns parameters
        • Remove columns example
      • Remove rows
        • Remove rows parameters
        • Remove rows example
      • Rename columns
        • Rename columns parameters
        • Rename columns example
      • Reorder columns
        • Reorder columns parameters
        • Reorder columns example
      • Split rows
        • Split rows parameters
        • Split rows example
    • Remodel summarizations
      • Summarize column names
        • Summarize column names parameters
        • Summarize column names example
      • Summarize column values
        • Summarize column values parameters
        • Summarize column values example
      • Summarize definitions
        • Summarize definitions parameters
        • Summarize definitions example
      • Summarize HED tags
        • Summarize HED tags parameters
        • Summarize HED tags example
      • Summarize HED type
        • Summarize HED type parameters
        • Summarize HED type example
      • Summarize HED validation
        • Summarize HED validation parameters
        • Summarize HED validation example
      • Summarize sidecar from events
        • Summarize sidecar from events parameters
        • Summarize sidecar from events example
    • Remodel implementation
      • The PARAMS dictionary
      • Operation class constructor
      • The do_op implementation
      • The validate_input_data implementation
      • The do_op for summarization
      • Additional requirements for summarization
      • Validator implementation
        • Stage 0: top-level structure
        • Stage 1: operation dictionary format
        • Stage 2: operation dictionary values
        • Later validation stages
  • HED Python tools
    • HED Python tool installation
    • Jupyter notebooks for HED
      • Extract JSON template
      • Find event combinations
      • Merge spreadsheet into sidecar
      • Sidecar to spreadsheet
      • Summarize events
      • Validate BIDS dataset
      • Validate BIDS dataset with libraries
      • Validate BIDS datasets
  • HED JavaScript tools
    • Javascript tool installation
    • Javascript package organization
    • Javascript programmatic interface
  • HED MATLAB tools
    • Tool overview
      • The HED MATLAB interface
      • What to download
    • Using MATLAB HEDTools
      • Getting a HEDTools object
      • Calling a tool
      • Input of events
      • Input of sidecars
      • Assembling HED annotations
      • Searching HED annotations
    • MATLAB Python install
      • Installing Python
        • Step 1: Find Python
        • Step 2: Install Python if needed
        • Step 3: Connect Python to MATLAB
        • Step 4: Install HEDTools
      • MATLAB functions for Python
    • Additional demos
      • Calling HED remodeling tools
      • Web service MATLAB demos
        • Overview of service requests
        • Setting up a session from MATLAB
        • Creating a request structure
        • Making a service request
        • Decoding a service response
  • HED and EEGLAB
    • Installing HEDTools EEGLAB plugin
      • Method 1: EEGLAB Extension Manager:
      • Method 2: Download and unzip
    • Annotating datasets
      • Launching EEGLAB HEDTools
        • Tagging the events
      • Validation
    • HED-based epoching

Other resources:

  • Documentation summary
    • HED publications
      • Journal articles
      • Preprints
      • Book chapters
    • HED schema viewer
    • HED Websites
    • HED working documents
  • HED governance and decision-making
    • 1. Introduction
    • 2. HED mission statement
    • 3. HED organizational structure
      • HED Scientific Advisory Board
      • HED Working Group
      • HED Library Development Teams
      • HED Maintainers
      • HED Outreach
      • HED User Community
    • 4. HED processes
    • 5. Operational guidelines
    • 6. License
    • 7. Acknowledgments

Data resources:

  • HED schemas
    • HED schema basics
      • Tag forms
      • Types of schemas
    • Viewing schemas
    • Available schemas
      • The standard schema
      • The SCORE library
      • The LANG library
  • HED test datasets
    • eeg_ds002893s_hed
    • eeg_ds003645s_hed
    • eeg_ds003645s_hed_column
    • eeg_ds003645s_hed_inheritance
    • eeg_ds003645s_hed_library
    • eeg_ds003645s_hed_longform
    • eeg_ds004105s_hed
    • eeg_ds004106s_hed
    • eeg_ds004117s_hed_sternberg
    • fmri_ds002790s_hed_aomic
    • fmri_soccer21_hed
    • BIDS validation

Other HED resources:

  • Project homepage
  • HED YouTube channel
  • HED specification
  • HED ontology
  • Online tools
  • HEDTools API
  • Web deployment
  • Code of conduct
HED Resources
  • Search

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