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README.Rmd
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README.Rmd
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---
title: "EEG quality analysis pipeline"
author: "Douwe Horsthuis"
date: "`r Sys.Date()`"
output: github_document
---
[](https://github.com/DouweHorsthuis/EEG-quality-analysis/graphs/contributors) [](https://github.com/DouweHorsthuis/EEG-quality-analysis/network/members) [](https://github.com/DouweHorsthuis/EEG-quality-analysis/stargazers) [](https://github.com/DouweHorsthuis/EEG-quality-analysis/blob/master/LICENSE.txt) [](https://www.linkedin.com/in/douwe-horsthuis-725bb9188/)
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
**This EEG pipeline will both pre-process your data and give you a quality report afterwards that will look somewhat like this:**
<img src="images/data_quality.jpg" alt="jpg of the data" align="center" width="1040" height="598"/>
Made by [Douwe Horsthuis](https://github.com/DouweHorsthuis/) as part of the:
<img src="images/CNL_logo.jpeg" alt="Logo" align="center" width="286"/>
**Table of Contents**
1. [About the project](#about-the-project)
2. [The code](#the-code)
- [How to download the code and setup EEGLAB](#how-to-download-the-code-and-setup-eeglab)
- [How to prepare your data](#how-to-prepare-your-data)
- [How to setup the binlists for triggers](#how-to-setup-the-binlists-for-triggers)
- [How to prepare the code itself](#how-to-prepare-the-code-itself)
- [Readme files and promts](#readme-files-and-promts)
3. [Functions explained](#functions-explained)
- [readme_to_EEG](#readme_to_eeg)
- [eBridge](#ebridge)
- [Edf2Mat](#edf2mat)
- [newtimef](#newtimef)
- [edf_to_fig](#edf_to_fig)
4. [Notes, shortcommings upcoming additions](#notes-shortcommings-upcoming-additions)
## About the project
The goal of this project is to have a reliable EEG pipeline that can be used in an objective way to show the quality of a data set, while potentially also pre-processing EEG data. The main difference between this pipeline and [the one it was based on](https://github.com/DouweHorsthuis/EEG_to_ERP_pipeline_stats_R/) is that this one ends with a PDF file that gives you some insight in the data. [Click here for an example of what it can look like](images/example_data_quality.pdf). Part of the idea is that this allows for analysis data as it comes, and tells us if the basics of a paradigms are working, if the participants responses are accurate, when eye tracking is used if the participant is looking at the right spot. The whole pipeline is written in Matlab, and relies on EEGLAB and some EEGLAB plugins. More in-depth information below. Part of the idea is to incorporate notes taken by the person collecting the data, we refer to these notes as readme files.
**If you plan to use it, please cite**: Horsthuis, D. J., Francisco, A. A., De Sanctis, P., Beker, S., & Molholm, S. (2022). EEG-quality-analysis (Version 1.0.0) [Computer software]. <https://doi.org/10.5281/zenodo.7041685>
## The code
### How to download the code and setup EEGLAB
To download the code you can [click here](https://github.com/DouweHorsthuis/EEG-quality-analysis/archive/refs/heads/main.zip). The script you want to use is in the src folder, and you'll also need the functions from the same folder.
To download EEGLAB [go here](https://sccn.ucsd.edu/eeglab/download.php) and follow the instructions.
After downloading EEGLAB, you will need to install the ERPlab plugin and the Biosig plugin. You can find either by **opening EEGLAB**, click on **file** (left top corner of the gui) and click on **Manage EEGLAB extensions**.
*AFTER INSTALLING EEGLAB AND THE ERPLAB & BIOSIG PLUGINS*
In MATLAB add the folder with the functions to your path. You can do this manually by
1. Clicking **HOME** (left top corner)
2. **Set Path** (in the middle of the top panel)
3. **Add with Sub folders...**
4. Find where you have the function folder, you just downloaded, and add it.
### How to prepare your data
This script expect that your BDF files are organized in one folder per paradigm with sub folder for each participant. Which looks something like this:
[Paradigm name]
├── [IDparticipant1] \# folder of the first participant
├── [IDparticipant2] \# folder of the second participant
: :
└── [IDparticipantn] \# folder of participant n
In line 68 and 69 it will update the loading and saving place for each individual subject.
### How to setup the binlists for triggers
You need files that will explain what trigger represents what. We call these binlists. You will need to create 2 binlists. 1 to plot your ERPS and another to calculate your reaction times (RTs). You can find and example for each in the testing folder, but for more all information on how to make one from scratch [see this](https://github-wiki-see.page/m/lucklab/erplab/wiki/Assigning-Events-to-Bins-with-BINLISTER:-Tutorial).
### How to prepare the code itself
While the idea is that there is very few manual (and potential subjective) input, you will need to set some parameters.
**Updating variables inside MATLAB**
Line 10 to 42 all relate to information MATLAB wants from you. The first part you should set only 1 time and should be the same for each participant you run for that paradigm.
```{matlab Empty code}
subject_list = {'id'};% The ID for the particpant
load_path = ''; %will open individual folders based on subject ID
save_path = ''; %where will you save the data (something like 'C:\data\')
binlist_location='';%where do you store your data
logo_location= '';%if you want to add a logo you can add it here if not leave it empty
logo_filename=''; %filename + extention (eg.'CNL_logo.jpeg')
binlist_name=''; %name of the text file with your bins
rt_binlist = ''; %name of the reaction time binlist
rt_plot_n=; %which RT bins do you want to plot together (can only plot one group)
plotting_bins=; %the bins that should become ERPs
channels_names={}; %channels that you want plots for (
colors={}; %define colors of your ERPs (1 per bin), add - for solid line add -- for dashed line -. for dotted/dashed : for dotted
downsample_to=; % what is the sample rate you want to downsample to
lowpass_filter_hz=; %50hz filter
highpass_filter_hz=; %1hz filter
epoch_time = [];
baseline_time = [];
low_fq= ;%lowest frequency for time frequency plot (if you go lower than 3hz you will need a lot of data)
high_fq=; %highest frequency for time freq plot, should never be more than half your sampling or half your low pass
```
In the testing folder you can see an example where it is all filled out. It will all look something like this (of course with changes that will work for where you have your data and how you named it etc.)
```{matlab example code}
subject_list = {'10508'};% The ID for the particpant
load_path = 'C:\Users\dohorsth\Desktop\SFARI Behav\FAST\Data\'; %will open individual folders based on subject ID
save_path = 'C:\Users\dohorsth\Desktop\SFARI Behav\FAST\test\'; %where will you save the data (something like 'C:\data\')
binlist_location='C:\Users\dohorsth\Desktop\SFARI Behav\FAST\script\';
logo_location= 'C:\Users\dohorsth\Documents\GitHub\EEG-quality-analysis\images\';%if you want to add a logo you can add it here if not leave it empty
logo_filename='CNL_logo.jpeg'; %filename + extention (eg.'CNL_logo.jpeg')
binlist_name='binlist_fast_simple.txt'; %name of the text file with your bins
rt_binlist = 'binlist_fast_rt.txt'; %name of the reaction time binlist
rt_plot_n=1:4; %which RT bins do you want to plot together (can only plot one group)
plotting_bins=1:4; %the bins that should become ERPs
channels_names={'Cz' 'Pz' 'CPz' 'Po3' 'Poz' 'po4' 'o1' 'oz' 'o2'}; %channels that you want plots for (
colors={'k-' , 'r-' , 'b-' ,'g-' }; %define colors of your ERPs (1 per bin), add - for solid line add -- for dashed line -. for dotted/dashed : for dotted
downsample_to=256; % what is the sample rate you want to downsample to
lowpass_filter_hz=50; %50hz filter
highpass_filter_hz=1; %1hz filter
epoch_time = [-100 500];
baseline_time = [-50 0];
low_fq= 3;%lowest frequency for time frequency plot (if you go lower than 3hz you will need a lot of data)
high_fq=40;%highest frequency for time freq plot, should never be more than half your sampling or half your low pass
```
### Readme files and promts
After making all these changes, you should be able to run the code. The first thing that happens is that you get prompted some questions. These are specific to each participant, this is why you will need to answer them for each participant. In all cases you will see a question show up in the command window of MATLAB. You need to type your answer and hit Enter. In some cases you will be explained how you need to format your answer (e.g. for bad channels you need to write both within {} and each channel requires '' to make it into separate strings).
**Readme files** are files with information filled out by the person collecting data. You can find an example [by clicking here](https://github.com/DouweHorsthuis/EEG-quality-analysis/blob/main/testing/xxxx%20F.A.S.T.%20Response%20Task%20x-xx-xxxx%20README.txt). If MATLAB cannot find the readme file or some of the information inside it it will add more prompts to get the same information, but manually. Just like explained above.
## Functions explained
There are several functions that are being used. Since for pre-processing all these functions are native to EEGLAB see [our pipeline](https://github.com/DouweHorsthuis/EEG_to_ERP_pipeline_stats_R/) or check out the [EEGLAB website](https://eeglab.org/) for an in-dept explanation.
### readme_to_EEG
As mentioned [above](#readme-files-and-promts) we use readme files in the lab to write notes during data collection. These notes will have a lot of information that would help to say something about the quality of the EEG. Because of that we created a function, `[EEG]=readme_to_EEG(EEG,readme_yn,data_path,save_path_indv,subject_list{s});` It requires the structure `EEG`, this is where EEGLAB stores it's information, and it's where the functions adds the info. `Readme_yn`, is the result of a prompt that asks if there is a readme file (yes/no). `data_path` is the specific path to that persons data and `save_path_indv` is the same for saving. Lastly `subject_list{s}` is giving the subject number. All of these are auto created by the script. The readme file is loaded as on big string and we look for specific parts of the text to find the info we are looking for using MATLABS `extractBetween` function. This means that if we move the readme file around and change the template, we won't be able to extract data efficiently without updating this function.
### eBridge
`eBridge` is a function that uses the EEG structure and checks if there are channels that are bridged. The full explanation can be found [here](https://psychophysiology.cpmc.columbia.edu/software/eBridge/index.html). Or in [this paper](https://psychophysiology.cpmc.columbia.edu/pdf/alschuler2013a.pdf) that was written and resulted in the function. `bridge=eBridge(EEG)` gives us a structure in which `bridge.Bridged.Labels` gives us the labels of all the bridged channels. Later we use this to plot a figure of the location of bridged channels. **note that bridged channels are not deleted**.
### Edf2Mat
We use the `Edf2Mat` function to transform our eye tracking files (collected with SR-research's Eyelink-1000 eye tracker system) and turn it into a heat map of where the participant was looking on the screen.
### edf_to_fig
While we still use `EDF2Mat` to load the .edf files into MATLAB, we use a combination of their functions in `edf_to_fig`. `edf_to_fig` only needs the filepath to the .edf files. These need to be in separate folders per participant, because we loop through all the files in the folder and merge all files ending in .edf. After we have use parts of the code from different functions from `Edf2Mat` to create a heatmap that shows us where the participant was looking for the whole of the paradigm.
### newtimef
Because `newtimef` is a native EEGLAB function [all the explanation can be found here](https://eeglab.org/tutorials/08_Plot_data/Time-Frequency_decomposition.html). However, it is a new addition to the pipeline that might still need some extra testing on our side **so please use with caution and report bugs**. For now it works on 1 channel only, where it does a time frequency analysis for the length of your epochs. If you have 1 condition, you will be prompted this question, you will only get one plot. If you have 2, you will get a plot for both and a difference plot. If you have more, you will get an error because this is not possible for now. Further more, **be aware that if you have multiple bins in your binlist, the first one or first 2 will be selected and plotted, depended on how many conditions you chose**.
## Notes, shortcommings upcoming additions
### Shortcommings and upcoming additions
Please let us know if you notice anything that does not work. So far we have made the following updates:
1- including possible time frequency analysis
2- plotting the heatmap of all eye tracking files
3- fixing the `[EEG]=readme_to_EEG(EEG,readme_yn,data_path,save_path_indv,subject_list{s});` function that had minor issues.
### Notes
If you have suggestions, edits, or issues, please leave them [here](https://github.com/DouweHorsthuis/EEG-quality-analysis/issues), or e-mail me \@ [douwehorsthuis\@gmail.com](mailto:douwehorsthuis@gmail.com). This pipeline works for our lab,but that doesn't mean it cannot be improved so all input is always welcome and very much appreciated.
## Acknowledgements
- [Douwe Horsthuis](https://github.com/DouweHorsthuis)
- [Ana Francisco](https://www.linkedin.com/in/ana-alves-francisco-3798599a/)
- [Sophie Molholm](https://www.einsteinmed.edu/faculty/12028/sophie-molholm/)
- [Pierfilippo De Sanctis](https://einsteinmed.edu/faculty/12347/pierfilippo-de-sanctis/)
- [Shlomit Beker](https://einsteinmed.edu/faculty/15122/shlomit-nir-beker/)
- [John Foxe](https://www.urmc.rochester.edu/people/29722174-john-j-foxe)