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1 change: 1 addition & 0 deletions .lycheeignore
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<!-- This file lists all links/regex to be ignored by lychee in the link checker -->
https://www.sciencedirect.com/science/article/pii/S1053811921010387
https://www.sciencedirect.com/science/article/pii/S0010945221001106
https://www.sciencedirect.com/science/article/pii/S1388245717309069
(_anchor|-anchor)

3 changes: 2 additions & 1 deletion docs/source/BidsAnnotationQuickstart.md
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Expand Up @@ -363,6 +363,7 @@ Once you have a JSON sidecar template, you should edit in your event annotations
The following is an edited version of the
JSON template from the previous step containing a minimal set of HED annotations.

(excerpted-json-file-with-tags-anchor)=
`````{admonition} JSON sidecar with completed annotation.
:class: tip
```json
Expand Down Expand Up @@ -496,7 +497,7 @@ or in a tool such as Excel.
You may save the edited spreadsheet in either `.tsv` or `.xslx` format.

The following is the extracted spreadsheet corresponding to the
[**edited JSON sidecar above**](excerpted-json-file-with-tags).
[**edited JSON sidecar above**](excerpted-json-file-with-tags-anchor).

````{admonition} HED annotation table extracted from JSON sidecar template.
| **column_name** | **column_value** | **description** | **HED** |
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28 changes: 12 additions & 16 deletions docs/source/HedMatlabTools.md
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Expand Up @@ -454,9 +454,8 @@ See [**MathWorks Python Compatibility Docs**](https://www.mathworks.com/support/

The greatest difficulty for users who are unfamiliar with Python is
getting Python connected to MATLAB.
Once that is done, many of the standard `hedtools` functions have
[**MATLAB HED tool wrapper functions**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/hedtools_wrappers)
that take MATLAB variables as arguments and return either MATLAB variables or opaque objects that
Once that is done, many of the standard `hedtools` functions can be accessed through
method call that take MATLAB variables and return either MATLAB variables or opaque objects that
can be passed to other MATLAB functions.

Thus, once the setup is done, you don't have to learn any Python syntax to use the tools.
Expand Down Expand Up @@ -669,7 +668,6 @@ Using HEDTOOLS version: {'date': '2022-06-20T14:40:24-0500', 'dirty': False, 'er
```
````


### MATLAB functions for Python

The following table lists the relevant MATLAB functions that are available.
Expand Down Expand Up @@ -727,8 +725,6 @@ The remodeling file used in this example can be found at
See [**File remodeling quickstart**](FileRemodelingQuickstart.md)
and [**File remodeling tools**](FileRemodelingTools.md) for
additional information.
The wrapper functions are available on GitHub in
the [**hedtools_wrappers**](https://github.com/hed-standard/hed-examples/tree/develop/src/matlab_scripts/hedtools_wrappers) directory.

(web-service-matlab-demos-anchor)=
### Web service MATLAB demos
Expand All @@ -745,16 +741,16 @@ directory of the [**hed-matlab**](https://github.com/hed-standard/hed-matlab) Gi

The following MATLAB code demos are available to show how to access HED web services.

| Target | MATLAB source | Purpose |
| ------ |-----------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
| Overall | [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m) | Harness for running all demos. |
| Overall | [**demoGetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoGetServices.m) | List available services. |
| Events | [**demoEventServices.m**](https://raw.githubusercontent.com/hed-standard/hed-examples/main/hedcode/matlab_scripts/web_services_demos/demoEventServices.m) | Validation, conversion, sidecar generation. |
| Events | [**demoEventSearchServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventSearchServices.m) | Search, assembly. |
| Schema | *in progress* | For schema library developers. |
| Sidecars | [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSidecarServices.m) | Validation, conversion, extraction, merging. |
| Spreadsheets | [**demoSpreadsheetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSpreadsheetServices.m) | Validation, conversion. |
| Strings | [**demoStringServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoStringServices.m) | Validation, conversion. |
| Target | MATLAB source | Purpose |
| ------ |----------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
| Overall | [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m) | Harness for running all demos. |
| Overall | [**demoGetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoGetServices.m) | List available services. |
| Events | [**demoEventServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventServices.m) | Validation, conversion, sidecar generation. |
| Events | [**demoEventSearchServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventSearchServices.m) | Search, assembly. |
| Schema | *in progress* | For schema library developers. |
| Sidecars | [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSidecarServices.m) | Validation, conversion, extraction, merging. |
| Spreadsheets | [**demoSpreadsheetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSpreadsheetServices.m) | Validation, conversion. |
| Strings | [**demoStringServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoStringServices.m) | Validation, conversion. |


The [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m)
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2 changes: 1 addition & 1 deletion docs/source/HedOnlineTools.md
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Expand Up @@ -560,7 +560,7 @@ JSON sidecars, BIDS-style events files, and spreadsheets in `.tsv` or `.xlsx` fo
Support is also included for assembling the annotations for a BIDS-style
events file with a JSON sidecar and for generating a template of a JSON sidecar from a BIDS events file.

The [**web_services**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services)
The [**web_services_demos**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services_demos)
directory in the `hed-examples` GitHub repository provides MATLAB examples of how to call these
services in MATLAB.

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2 changes: 1 addition & 1 deletion docs/source/HedPythonTools.md
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Expand Up @@ -43,7 +43,7 @@ and an online version of the tools.
The [**Create a JSON template**](https://hed-examples.readthedocs.io/en/latest/BidsAnnotationQuickstart.html#create-a-json-template) tutorial provides a step-by-step tutorial for using the online tool
that creates a template based on the information in a single `events.tsv` file.
For most datasets, this is sufficient.
In contrast, the [**extract_json_template.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/extract_json_template.ipynb)
In contrast, the [**extract_json_template.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb)
Jupyter notebook bases the extracted template on the entire dataset.

To use this notebook, substitute the specifics of your BIDS
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2 changes: 1 addition & 1 deletion docs/source/HedSchemas.md
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Expand Up @@ -92,7 +92,7 @@ directory of the [**hed-schemas**](https://github.com/hed-standard/hed-schemas)

### The SCORE library

The HED SCORE library is an implementation of the [**SCORE**](https://www.sciencedirect.com/science/article/pii/S1388245717309069?via%3Dihub) standard for clinical annotation of EEG by neurologists.
The HED SCORE library is an implementation of the [**SCORE**](https://www.sciencedirect.com/science/article/pii/S1388245717309069) standard for clinical annotation of EEG by neurologists.
For more information and the latest references see
[**HED SCORE schema**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/README.md).

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2 changes: 1 addition & 1 deletion docs/source/HowCanYouUseHed.md
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Expand Up @@ -616,7 +616,7 @@ for more information on installation and use.
The project source code is located in the [**CTagger**](https://github.com/hed-standard/ctagger) GitHub repository.
<p></p>

[*MATLAB HedTools**](https://www.hed-resources.org/en/latest/MatlabHedTools.md) explains how the
[*HED MATLAB Tools**](https://www.hed-resources.org/en/latest/HedMatlab.md) explains how the
users can use the HEDTools in MATLAB using one of three approaches: using MATLAB wrappers for the HED Python tools,
using MATLAB wrappers for the HED web services, or by calling HED tools through EEGLAB.

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3 changes: 2 additions & 1 deletion docs/source/index.rst
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Expand Up @@ -86,7 +86,8 @@ San Diego (UCSD) under funding by The Swartz Foundation and by U.S. National Ins

Further **HED (Gen 2, 4.0.0 <= version < 8.0.0)** development led by Kay Robbins
of the University of Texas San Antonio was
funded by The Cognition and Neuroergonomics Collaborative Technology Alliance (CaN CTA) program of U.S Army Research Laboratory (ARL) under Cooperative Agreement Number W911NF-10-2-0022.
funded by The Cognition and Neuroergonomics Collaborative Technology Alliance (CaN CTA) program
of U.S Army Research Laboratory (ARL) under Cooperative Agreement Number W911NF-10-2-0022.

**HED (Gen 3, version >= 8.0.0)** is now maintained and further developed by the
HED Working Group led by Kay Robbins and Scott Makeig with Dung Truong, Monique Denissen,
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20 changes: 10 additions & 10 deletions src/jupyter_notebooks/bids/README.md
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Expand Up @@ -5,16 +5,16 @@ validating, summarizing, and analyzing your BIDS datasets.

**Table 1:** Useful Jupyter notebooks for processing BIDS datasets.

| Notebooks | Purpose |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------|
| [`extract_json_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_sidecar.ipynb) | Creates a JSON sidecar based on all the event files in a dataset. |
| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb) | Creates a spreadsheet of unique combinations of event values. |
| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/bids_merge_sidecarmerge_spreadsheet_into_sidecar.ipynb) | Merges a spreadsheet version of a sidecar into a JSON sidecar. |
| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. |
| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) | Summarizes the contents of the event files, including value counts. |
| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb) | Validates the HED annotations in a BIDS dataset. |
| [`validate_bids_dataset_with_libraries`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb) | Demonstrates use of HED libraries in validation. |
| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) | Validates the HED annotations in a list of BIDS datasets. |
| Notebooks | Purpose |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------|
| [`extract_json_template`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb) | Creates a JSON sidecar based on all the event files in a dataset. |
| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb) | Creates a spreadsheet of unique combinations of event values. |
| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/merge_spreadsheedt_into_sidecar.ipynb) | Merges a spreadsheet version of a sidecar into a JSON sidecar. |
| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. |
| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) | Summarizes the contents of the event files, including value counts. |
| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb) | Validates the HED annotations in a BIDS dataset. |
| [`validate_bids_dataset_with_libraries`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb) | Demonstrates use of HED libraries in validation. |
| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) | Validates the HED annotations in a list of BIDS datasets. |

These notebooks require HEDTools, which can be installed using `pip` or directly.

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