The NeuroStimulation App (nestapp) uses EEGLAB and TESA functions to automatically clean the TMS-EEG data.
The nestapp has been developed using MATLAB App Designer (R2023b & R2018a). The idea is to use the currently available EEGLAB (v10.02), TESA (v1.1.1), and FastICA (2.5) functions, for cleaning and analyzing TMS-EEG data. Note that FastICA should be added to your Matlab path.
1- After downloading the app, run nestapp.m.
2- On the left panel, you will see a list of steps that you can choose to apply to your data. By clicking on each step, extra information including the function name, will be available in the 'Info' section. Please read the extra information about each function, on EEGLAB, TESA, and FastICA websites:
EEGLAB: https://eeglab.org/ TESA: https://nigelrogasch.gitbook.io/tesa-user-manual/ FastICA: http://research.ics.aalto.fi/ica/fastica/index.shtml
3- You can use the 'Add', 'Remove', 'Move Up' and 'Move Down' buttons to create your desired cleaning pipeline in the 'Selected Steps'. Each of the steps may have parameters that you wish to modify. You can change the value for appropriate properties in the panel below the 'Parameter(s)' section by clicking on the value for appropriate properties. The 'Default Value' button will reset the values of the selected step into the default values.
4- You can save the created pipeline for future uses, by clicking 'Save pipeline' and giving it the desired name. The pipeline will be saved as a MATLAB Mat file. The 'Load Pipeline' will load the pipeline into the 'Selected Steps' section.
5- In the right panel, if EEGLAB is not in your MATLAB path, you can select the folder containing the EEGLAB package.
6- In the 'Select data to perform Analysis' section, choose the files ( in *.vhdr, *.set, *.cnt, *.cdt format) you want to apply the analysis. the number of selected files and the index of the current file being processed will appear below.
7- Pressing 'Re/Start Steps' will erase all selected steps and changes made to the parameters.
8- By pressing the 'Run Analysis' the cleaning and analyzing process will be started.
NOTE: In case your data doesn't have a channel location and you would like to use 'Load Channel Location', please make sure that this function is performing right. Extra features will be added in future.
Aref Pariz: The developed code (v1.0 2023) was a part of my job at the Royal Institute for Mental Health, in Dr. Sara Tremblay's lab (NESTLAB: https://www.nest-lab.ca/) and Dr. Jeremie Lefebvre's Lab at the University of Ottawa.