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-(eeglab-integration-anchor)=
-## EEGLAB plug-in integration
-EEGLAB is the most widely used EEG software environment for analysis of
-human electrophsyiological (and related) data.
-EEGLAB combines graphical and command-line user interfaces,
-making it friendly for both beginners who may who prefer a visual,
-and automated way of analyzing data as well as experts,
-who can easily customize, extend, and automate the EEGLAB tool environment by writing new
-EEGLAB-compatible scripts and functions.
-
-HED is fully integrated into EEGLAB via the *HEDTools* plug-in, allowing users to annotate their
-EEGLAB STUDY and datasets with HED,
-as well as enabling HED-based data manipulation and processing.
-
-### Installing *HEDTools*
-
-*HEDTools* EEGLAB plug-in can be installed using one of the following ways:
-
-#### Method 1: EEGLAB Extension Manager:
-
-Launch EEGLAB. From the main GUI select:
-
-> **File --> Manage EEGLAB extension**
-
-The extension manager GUI will pop up.
-
-From this GUI look for and select the plug-in *HEDTools* from the main window,
-then click into the *Install/Update* button to install the plug-in.
-
-
-#### Method 2: Download and unzip
-
-Download the zip file with the content of the plug-in *HEDTools* either from
-[**HED Matlab EEGLAB plugins**](https://github.com/hed-standard/hed-matlab/blob/master/EEGLABPlugin)
-or from the EEGLAB [**plug-ins summary page**](https://sccn.ucsd.edu/eeglab/plugin_uploader/plugin_list_all.php).
-
-Unzip file into the folder *../eeglab/plugins* and restart the *eeglab* function in a MATLAB session.
-
-(annotating-datasets-anchor)=
-### Annotating datasets
-
-We will start by adding HED annotations to the EEGLAB tutorial dataset.
-
-After installing the *HEDTools* open the EEGLAB main window and load the dataset by selecting the menu item:
-
-> **File --> Load existing dataset** .
-
-Selecting the tutorial dataset under your eeglab installation _eeglab/sample_data/eeglab_data.set_.
-
-Read a description of the dataset and of its included event codes by selecting:
-
-> **Edit --> About this dataset**:
-
-
-
-The description gives a general idea of the codes found in the event structure.
-Yet, inquisitive researchers interested in the nature of the stimuli
-(e.g., color and exact location of the squares on the screen)
-would have to look up the referenced paper for details.
-
-Our goal in using HED tags is to describe the experimental events that are recorded
-in the *EEG.event* data structure in sufficient detail that anyone using the dataset
-in the future will not need to find and read a separate, detailed description of the dataset
-or study to understand the recorded experimental events.
-As demonstrated below, such annotation will allow us to extract epochs using meaningful
-HED tags instead of the alpha-numeric codes often associated with shared EEG data.
-
-#### Launching EEGLAB HEDTools
-To add and view HED tags for the dataset, from EEGLAB menu, select:
-
-> **Edit --> Add/Edit event HED tags**.
-
-_HEDTools_ will extract information from the *EEG.event* structure,
-automatically detecting the event structure fields and their unique values.
-
-The _HEDTools_ ignore the fields the event structure fields *.latency*, *.epoch*, and *.urevent*.
-
-A window will appear asking you to verify/select categorical fields:
-
-
-
-Here both *position* and *type* are categorical fields.
-*HEDTools* automatically selects fields with less than 20 unique values to be categorical,
-but the user can modify which values are chosen.
-
-CTagger (for 'Community Tagger') is a graphical user interface (GUI) built to facilitate
-the process of adding HED tags to recorded events in existing datasets.
-Clicking *Continue* brings up the *CTagger* interface:
-
-
-
-The CTagger GUI is organized using a split window strategy.
-The left window shows the items to be tagged,
-and the right window shows the current HED tags associated with the selected item.
-The *Show HED schema* button brings up a browser for the HED vocabulary.
-
-Through the CTagger GUI, users can explore the HED schema,
-quickly look up and add tags (or tag groups) to the desired event codes,
-and use import/export features to reuse tags on from other data recordings in the same study.
-
-The process of tagging is simply choosing tags from the available vocabulary
-(using the HED schema browser) and associating these tags with each event code.
-
-Once familiar with HED and the vocabulary, most users just type the tags directly in the tag window
-shown on the right.
-
-CTagger is used as part of the HEDTools plug-in in this tutorial,
-but it can also be used as a standalone application.
-
-Instructions on downloading and using the standalone version of CTagger,
-as well as step-by-step guide on how to add HED annotation with CTagger,
-can be found at in [**Tagging with CTagger**](./TaggingWithCTagger.md).
-
-#### Tagging the events
-A brief step-by-step guide to selecting tags can be found at
-[**HED annotation quickstart**](./HedAnnotationQuickstart.md).
-The following shows example annotations using the process suggested in the quickstart. we will import the annotation saved in the _events.json file format.
-Download the file [**eeglab-tutorial_events.json**](./_static/data/eeglab-tutorial_events.json) then select:
-
-> **File --> Import --> Import BIDS events.json file**
-
-to import it to CTagger. You can now review all the tags via:
-
-> **File --> Review all tags**
-
-
-
-#### Validation
-The last step of the annotation process is to validate the HED annotations.
-Click on the *Validate all* button at the bottom pane.
-A window will pop up showing validation results.
-If there are issues with the annotation, there will be a line for each of the issues found.
-
-Here is an example of validation log file with issues:
-
-
-
-If the annotation was correct, a message will appear confirming the validity:
-
-
-
-Click *Finish* on the main CTagger window to end the annotation.
-
-The tag review window will show up again for a final review and the option to save
-the annotation into an _events.json file for distribution just as with the *eeglab-tutorial_events.json*.
-Hit *Ok* to continue after that.
-
-A last window will pop up asking what you would like to overwrite the old dataset with the
-tagged one or save new dataset as a separate file. Click **Ok** when you're done.
-
-
-
-You just finished tagging! *HEDTools* generates the final HED string for each event
-by concatenating all tags associated with the event values of that event (separated by commas).
-The final concatenated version is put the string in a new field **HED** in EEG.event.
-
-### HED-based epoching
-
-The EEGLAB *pop_epoch* function extracts data epochs that are time locked to specified event types.
-This function allows you to epoch on one of a specified list of event types as defined by the
-*EEG.event.type* field of the EEG structure.
-
-*HEDTools* provides a simple way for extracting data epochs from annotated datasets using
-a much richer set of conditions.
-To use HED epoching, you must have annotated the EEG dataset.
-
-If the dataset is not tagged, please refer to [Annotating datasets](#annotating-datasets)
-on how to tag a dataset.
-
-Start by choosing the menu option:
-
-> **Tools --> Extract epochs by tags**:
-
-
-
-
-This will bring up a window to specify the options for extracting data epochs:
-
-
-
-The *pop_epochhed* menu is almost identical to the EEGLAB *pop_epoch* menu with the
-exceptions of the first input field (**Time-locking HED tag(s)**) and the second
-input field (**Exclusive HED tag(s)**).
-
-Instead of passing in or selecting from a group of unique event types,
-the user passes in a comma separated list of HED tags.
-For each event all HED tags in this list must be found for a data epoch to be generated.
-
-Clicking the adjacent button (with the label …) will open a search tool to help you select
-HED tags retrieved from the dataset.
-
-
-
-When you type something in the search bar, the dialog displays a list below containing possible matches.
-Pressing the "up" and "down" arrows on the keyboard while the cursor is in the search bar moves to the
-next or previous tag in the list.
-
-Pressing "Enter" selects the current tag in the list and adds the tag to the search bar.
-You can continue search and add tags after adding a comma after each tag.
-When done, click the **Ok** button to return to the main epoching menu.