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Hierarchical Event Descriptors

Hierarchical Event Descriptors (HED) are a controlled vocabulary of terms describing events in a machine-actionable form so that algorithms can use the information without manual recoding. HED annotation can be used to describe any experimental events by combining information from the dataset's events.tsv files and events.json sidecars.

HED annotations and vocabulary

A HED annotation consists of terms selected from a controlled hierarchical vocabulary (the HED schema). Individual terms are comma-separated and may be grouped using parentheses to indicate association. See https://www.hedtags.org/display_hed.html to view the HED schema and the HED resources site for additional information.

Starting with HED version 8.0.0, HED allows users to annotate using individual terms or partial paths in the HED vocabulary (for example Red or Visual-presentation) rather than the full paths in the HED hierarchy ( Property/Sensory-property/Sensory-attribute/Visual-attribute/Color/CSS-color/Red-color/Red or Property/Sensory-property/Sensory-presentation/Visual-presentation).

HED specific tools MUST treat the short (single term) and long (full path) HED tag forms interchangeably, converting between the forms when necessary based on the HED schema. Examples of test datasets using the various forms can be found in hed-examples/datasets on GitHub. Using the short form for tags is strongly RECOMMENDED whenever possible.

Annotating events

Event-related data in BIDS appears in tab-separated value (events.tsv) files in various places in the dataset hierarchy (see Events).

events.tsv files MUST have onset and duration columns. Dataset curators MAY also include additional columns and define their meanings in associated JSON sidecar files (events.json).

Example: An excerpt from an events.tsv file containing three columns (trial_type, response_time, and stim_file) in addition to the required onset and duration columns.

onset  duration  trial_type  response_time stim_file
1.2    0.6       go          1.435         images/red_square.jpg
5.6    0.6       stop        1.739         images/blue_square.jpg

The trial_type column in the above example contains a limited number of distinct values (go and stop). This type of column is referred to as a categorical column, and the column's meaning can be annotated by assigning HED tags to describe each of these distinct values. The JSON sidecar provides a JSON object of annotations for these categorical values. That is, the object is a dictionary mapping the categorical values to corresponding HED annotations.

In contrast, the response_time and stim_file columns could potentially contain distinct values in every row. These columns are referred to as value columns and are annotated by creating a HED tag string to describe a general pattern for these values. The HED annotation for a value column must include a # placeholder, which dedicated HED tools MUST replace by the actual column value when the annotations are assembled for analysis.

Example: An accompanying events.json sidecar describing both categorical and value columns of the previous example. The duration column is also annotated as a value column.

{
  "Duration": {
    "LongName": "Image duration",
    "Description": "Duration of the image presentations",
    "Units": "s",
    "HED": "Duration/# s"
  },
  "trial_type": {
    "LongName": "Event category",
    "Description": "Indicator of type of action that is expected",
    "Levels": {
      "go": "A blue square is displayed to indicate starting",
      "stop": "A red square is displayed to indicate stopping"
    },
    "HED": {
          "go": "Sensory-event, Visual-presentation, (Square, Blue)",
          "stop": "Sensory-event, Visual-presentation, (Square, Red)"
       }
   },
   "response_time": {
       "LongName": "Response time after stimulus",
       "Description": "Time from stimulus presentation until subject presses button",
       "Units": "ms",
       "HED": "(Delay/# ms, Agent-action, (Experiment-participant, (Press, Mouse-button))),"
   },
   "stim_file": {
       "LongName": "Stimulus filename",
       "Description": "Relative path of the stimulus image file",
       "HED": "Pathname/#"
   }
}

Dedicated HED tools MUST assemble the HED annotation for each event (row) by concatenating the annotations for each column, along with the annotation contained directly in a HED column of that row as described in the next section.

Example: The fully assembled annotation for the first event in the above events.tsv file with onset 1.2 (the first row) is:

Duration/0.6 s, Sensory-event, Visual-presentation, (Square, Blue),
(Delay/1.435 ms, Agent-action, (Experiment-participant, (Press, Mouse-button))),
Pathname/images/red_square.jpg

Annotation using the HED column

Another tagging strategy is to annotate individual events directly by including a HED column in the events.tsv file. This approach is necessary when each event has annotations that are unique and do not fit into a standard set of patterns, such as during manual annotation of artifacts or signal features.

Some acquisition or presentation software systems may produce individual annotations for each event during the experiment. These individualized annotations may be placed into the HED column of the events.tsv file when the data is converted into BIDS format.

Dedicated HED tools that assemble the full annotation for events MUST not distinguish between HED annotations extracted from events.json sidecars and those appearing in the HED column of events.tsv files. The HED strings from all sources are concatenated to form the final event annotations.

Annotations placed in sidecars are the RECOMMENDED way to annotate data using HED. These annotations are preferred to those placed directly in the HED column, because they are simpler, more compact, more easily edited, and less prone to inconsistencies.

HED and the BIDS inheritance principle

Most studies have event files whose columns contain categorical and numerical values that are similar across the recordings in the study. If possible, users should annotate these columns in a single events.json sidecar placed at the top level in the dataset.

If some recordings in the dataset have a column whose values deviate from a standard pattern, then the annotations for that column MUST be placed in sidecars located deeper in the dataset directory hierarchy. According to the BIDS Inheritance Principle, once a column key in a sidecar (that is, the column name found in the events.tsv files) is set, information about that column cannot be overridden by a sidecar appearing in a directory closer to the dataset root.

HED schema versions

The HED vocabulary is specified by a HED schema, which delineates the allowed HED path strings. The version of HED used in tagging a dataset should be provided in the HEDVersion field of the dataset_description.json file located in the dataset root directory. This allows for a proper validation of the HED annotations (for example using the bids-validator).

Example: The following dataset_description.json file specifies that the HED8.1.0.xml file from the standard_schema/hedxml directory of the hed-schemas repository on GitHub should be used to validate the study event annotations.

{
  "Name": "A great experiment",
  "BIDSVersion": "1.7.0",
  "HEDVersion": "8.1.0"
}

If you omit the HEDVersion field from the dataset description file, a warning will be generated and any present HED information will be validated using the latest version of the HED schema. This is bound to result in problems, and hence, it is strongly RECOMMENDED that the HEDVersion field be included when using HED in a BIDS dataset.

Using HED library schemas

HED also allows you to use one or more specialized vocabularies along with or instead of the standard vocabulary. These specialized vocabularies are developed by communities of users and are available in the GitHub hed-schemas repository. Library schema are specified in the form <library-name<_>library-version>.

Example: The following dataset_description.json file specifies that the HED8.1.0.xml standard schema should be used along with the SCORE library for clinical neurological annotation located at HED_score_1.0.0.xml.

{
  "Name": "A great experiment",
  "BIDSVersion": "1.7.0",
  "HEDVersion": ["8.1.0", "sc:score_1.0.0"]
}
The sc: is a user-chosen prefixes used to distinguish the sources of the terms in the HED annotation. The prefixes MUST be alphanumeric. Any number of prefixed schemas may be used in addition to a non-prefixed one.

The following HED annotation from this dataset uses the sc: prefix with Photomyogenic-response and Wicket-spikes because these terms are from the SCORE library, while Data-feature is from the standard HED schema.

Data-feature, sc:Photomyogenic-response, sc:Wicket-spikes

If only one schema is being used for annotation, the prefix can be omitted entirely. The following dataset_description.json indicates that only the SCORE library version 0.0.1 will be used for HED annotation in this dataset.

{
  "Name": "A great experiment",
  "BIDSVersion": "1.7.0",
  "HEDVersion": "score_1.0.0"
}

The corresponding notations in the dataset do not have a prefix:

Photomyogenic-response, Wicket-spikes