csc-eeg-tools

Set of matlab functions for EEG io, preprocessing, analysis from the Center for Sleep and Consciousness, University of Wisconsin (csc)

csc-eeg-tools

This set of functions is designed to be used as quick tools in matlab for eeg processing The tools can be used on their own or by using one of the template files provided

Get the code

To get the latest code using git, simply type:

git clone https://github.com/CSC-UW/csc-eeg-tools.git

Installation

1. download zip file
2. extract and save under your prefered path
3. add the path to matlab and you're ready to go

Key-Shortcuts for Plotter

Navigation

Usage	Shortcut
number of displayed channels	ctrl + d
change epoch length	ctrl + e
toggle components/channels	ctrl + t
set filter parameters	ctrl + f
move to next epoch	arrow right
move to previous epoch	arrow left
move right (not a full epoch)	ctrl + arrow right
move left (not a full epoch)	ctrl + arrow left
move down to next channel section	page up
move up to previous channel section	page down
set event marker	use keyboard numbers to place event at mouse position
set event marker alternative	right mouse click and use context menu
delete event marker	left mouse click on the event marker

View

Usage	Shortcut
increase channel scale	arrow up
decrease channel scale	arrow down
hide/show dotted vertical grid	g
hide/show dotted horizontal grid	h
set vertical scale spacing	ctrl + g
set horizontal grid spacing	ctrl + h
hide / mark channels	click on channel label
toggle negative up/down	ctrl + n

Tools

Usage	Shortcut
load eeg	ctrl + l
save eeg	ctrl + s
export hidden channels	ctrl + x
export marked trials	ctrl + t

How to sleep score using the plotter

Open the csc_eeg_plotter(EEG), you will likely want to adjust the montage to match a more typical sleep scoring montage (e.g. F3-A2).

For classic sleep scoring, change the mode in the tools menu and use the numbers on the keyboard to mark the stages (wake should be number 6, not 0). You can mark arousal beginnings and end using the number 4 (since there is no NREM4 anymore).

For continuous sleep scoring simple place a marker at the beginning of the stage transition (keyboard number at mouse position).

If there is a long period prior to sleep that should not be considered for scoring (e.g. lights on), then simply begin scoring at a later epoch.

Once your scoring is complete, you can use the function csc_events_to_hypnogram to produce a table and convert into stages stored in EEG.swa_scoring.stages. You should probably also save the events to file just in case (using the event menu in the plotter).

How to use the functions

in this example we assume EEG is you loaded dataset:

to open the plotter and check e.g. for artifacts and hide bad channels use the code

` EEG = csc_eeg_plotter(EEG); `

to change the hidden channels to bad channels use

` EEG.bad_channels{1} = EEG.hidden_channels; `

to reject/delete channels with artifacts

` EEG = pop_select(EEG, 'nochannel', EEG.bad_channels{1}); `

if you have run e.g. ICA on your dataset and want to look/remove components

open the plotter and also the component plot for each channel

` csc_eeg_plotter(EEG); EEG.good_components = csc_component_plot(EEG); `

now to remove the marked bad components and automaticaly change the local eeg variable use

` EEG = pop_subcomp( EEG , find(~EEG.good_components)); EEG = eeg_checkset(EEG); ` you can also open the csc_eeg_plotter to visualise the components and also plot the channel activity as if the selected components had already been removed

Troubleshooting

Comments and suggestions are more than welcome, just create an issue in github with the specific question/suggestion