HED Resources
latest
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
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 search basics
Calling syntax
Single tag queries
Single-term search
Quoted-tag search
Tag-path with slash
Tag-prefix with wildcard
Logical queries
Group 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
File 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
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
File 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 do_op for summarization
Additional requirements for summarization
HED Python tools
Jupyter notebooks for HED in BIDS
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
Jupyter notebooks for data curation
Consistency of BIDS event files
Calling HED tools
Getting a list of files
Dictionaries of filenames
BIDS-specific dictionaries of files
A generic dictionary of filenames
Logging processing steps
HED JavaScript tools
Javascript tool installation
Javascript package organization
Javascript programmatic interface
HED MATLAB tools
HED services in MATLAB
Overview of service requests
Setting up a session from MATLAB
Creating a request structure
Making a service request
Decoding a service response
EEGLAB plug-in integration
Installing
HEDTools
Method 1: EEGLAB Extension Manager:
Method 2: Download and unzip
Annotating datasets
Launching EEGLAB HEDTools
Tagging the events
Validation
HED-based epoching
Python HEDTools in MATLAB
Getting started
Step 1: Find Python
Step 2: Install Python if needed
Step 3: Connect Python to Matlab
Step 4: Install HEDTools
MATLAB wrappers for HEDTools
Direct calls to HEDTools
Calls to HED remodeling tools
MATLAB functions for Python
Data resources:
HED schemas
HED schema basics
Tag forms
Types of schemas
Viewing schemas
Available schemas
The standard schema
The SCORE library
The LISA 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
Drafts:
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
Other HED resources:
Project homepage
HED YouTube channel
Documentation summary
Specification
Online tools
HEDTools API
Web deployment
Code of conduct
HED Resources
Index
Edit on GitHub
Index
Read the Docs
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