The EEG Newsletter #11

Choosing EEG analysis software

Welcome to The EEG Newsletter!

Every two weeks I share news from our community of EEG researchers, vacancies, events and other interesting EEG-related stuff. Subscription is free.

In this edition

Choosing EEG analysis software
Events
Vacancies

Choosing EEG analysis software

When we start out doing EEG analysis, we’ll often use the software our supervisor is familiar with and not give it a second thought. At first this is fine, but the choice of software is not inconsequential. It imposes constraints and offers opportunities. Since it takes considerable time and effort to learn any new software, it is definitely worth investing a bit more attention to picking the one that’s right for you.

Below I’ve listed 5 well known packages with some pros and cons. Brainstorm is the only one I haven’t used myself. I’d be excited to hear if anyone has anything to add!

EEGLAB

EEGLAB is an open-source Matlab toolbox for processing EEG, MEG and other electro-physiological data. It provides a GUI and for experienced Matlab users, EEGLAB offers a structured programming environment for storing and accessing data. It offers an open-source platform through which people can share new plug-ins.

Pros:

1. One thing I love about EEGLAB is that you can give commands using the GUI, but then get the code for it. That way you can use the GUI at first and slowly evolve to creating custom scripts.

2. Its very straightforward to create custom scripts combining EEGLAB functions with functions from the MATLAB ecosystem, and also other toolboxes (such as Fieldtrip and Brainstorm).

3. EEGLAB has a large and active user community and forum. Its very easy to find resources, tutorials, and support.

Cons:

1. EEGLAB runs on MATLAB which is not open-source and the license is expensive.

2. While EEGLAB comes with a GUI, you need to be a bit more tech savvy than for fully GUI-based software such as Brain Vision Analyzer.

3. Another not-so-great characteristic of EEGLAB is that running (for example) an ICA takes foreeever. MNE is much (orders of magnitude) faster. I’ve not tested ICA with other packages.

MNE-Python

MNE-Python is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, NIRS, and more. It does not have a GUI, instead all functionality is available through scripting.

Pros:

1. MNE Python is open source and so is Python.

2. It easily integrates with other Python libraries such as NumPy, SciPy, Pandas, and scikit-learn. This makes MNE super flexible and enables advanced data analysis, machine learning, and visualization.

3. It’s fast!

Cons:

1. Learning MNE can take quite some time and effort, especially if you are not familiar with Python.

2. What I find to be the worst aspect of using MNE is inherent to any Python based toolbox: you spend a lot of time on updates and all the random misery that accompanies them.

3. Although there is documentation and tutorials available, I don’t find it to be very user friendly, especially for beginners.

Fieldtrip

FieldTrip is an open-source MATLAB toolbox for MEG, EEG and iEEG analysis. It contains a set of high-level functions, and does not have a GUI. The toolbox functions can be combined into an analysis pipeline, i.e. a MATLAB script containing all steps of your analysis.

Pros:

1. It supports various data preprocessing techniques, time-frequency analysis, connectivity analysis, source reconstruction, and statistical analysis.

2. FieldTrip offers a flexible and modular framework.

3. Its very straightforward to create custom scripts combining Fieldtrip functions with functions from the MATLAB ecosystem, and also other toolboxes (such as EEGLAB and Brainstorm).

Cons:

1. Fieldtrip runs on MATLAB which is not open-source and the license is costly.

2. Fieldtrip has no GUI, and learning Fieldtrip takes time and effort, especially if you are new to MATLAB. Understanding the toolbox's structure, syntax, and implementing custom analyses is not straightforward.

3. Although there is documentation and tutorials available, I don’t find it to be very user friendly, especially for beginners.

Brainstorm

Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.

Pros:

1. Brainstorm has a rich and intuitive GUI, which does not require any programming knowledge. It also has some pre-defined analysis pipelines, which makes it easier to get started if you don’t have a lot of experience.

2. It offers advanced source localization techniques such as distributed source imaging, cortically-constrained source imaging, and functional connectivity analysis.

3. Although Brainstorm is developed with Matlab (and Java), it does not require users to own a Matlab license.

Cons:

1. It excels in source localization, but has relatively limited functionality in other EEG analysis domains.

2. Brainstorm offers a user-friendly interface, but using more advanced features may still require some scripting.

Brain Vision Analyzer

BrainVision Analyzer is a commercial software package designed specifically for EEG analysis. It is fully GUI-based and has tools for data preprocessing, artifact correction, spectral analysis, event-related potentials (ERPs), and statistics.

Pros:

1. It’s very user friendly and is an easy and attractive way to get into EEG analysis.

   The interface provides a visual representation of the analysis pipeline, allowing for easy navigation and parameter adjustments.

2. No coding experience needed whatsoever.

Cons:

1. Since its all happening “under the hood”, it does not offer as good an insight into the analysis steps as a scripted analysis pipeline may do.

2. BrainVision Analyzer is a commercial software, which means it requires a license.

3. It has limited flexibility and customization options compared to open-source tools or programming-based approaches. Integration with other packages is not really an option.

Apart from each toolbox’s peculiarities, I think the two most defining questions to ask yourself are:
1.- Do I want to learn how to code or do I prefer using a GUI?
2.- Do I want to learn MATLAB or Python?
We can talk about this another time, but if you already have a (partial) answer to those questions, that will help a lot.

Events

June 6th, 2023, ESI Talks - Bradley Voytek, Frankfurt, DE
The physiology and function of aperiodic neural activity

June 27-30, 2023, International Multisensory Research Forum, Brussels, BE

June 30th - July 2nd, 2023, Body-Brain Waves, Salerno, IT
Body-Brain physiological waves meet the waves of the Amalfi Coast

July 13-14, 2023, Salzburg Mind-Brain Annual Meeting (SAMBA), AT

September 14-15, 2023 mbt Conference 2.0 , Belgrade, RS
Methods in Mobile EEG

September 27-29, Multimodal EEG Workshop (TMS-EEG), Milan, IT
Integrating EEG and neuronavigated TMS techniques

October 16-19, 2023 Cutting Gardens 2023 (M)EEG methods conference
This multi-hub meeting is all about cutting edge (M)EEG methods. Hubs (gardens) are sprouting in Ghent (BE), Berlin (DE), Donostia (San Sebastián, ES), Belgrade (CS), Nijmegen (NL), Bornemouth (UK), Lyon (FR), Paraná (AR), Santiago (CL), San Diego (US), Montréal (CA), La Habana (CU), Dundee (SC), Caen (FR), Genova (IT), Roma (IT), Regensburg (DE), Chengdu (CN).

Vacancies

• Florida State University, US - Neural oscillations in cognitive control and mood disorders- Post-Doc, PhD, lab manager and RA's.

PhD

• University of Bern, CH - System Neuroscience & Sleep.

• Ghent University, BE - Interactions between (chronic) pain, cognitive functioning, and effort-based decision-making.

• University of Birmingham, UK - Oscillatory and anatomical phenotypes for assessment of brain health.

• Birkbeck University of London, UK - Neural synchrony in collaborating preschoolers.

• Vrije Universiteit, Amsterdam, NL - The neural basis of hypnosis.

• University of Iceland in Reykjavik - PhD or Postdoc position at the Icelandic Vision Lab.

• University of Birmingham, UK - A developmental lifespan perspective on neural plasticity in learning strategies.

• Philipps Universität Marburg, DE - Several PhD positions.

• University of Birmingham, UK - Oscillatory and anatomical phenotypes for assessment of brain health.

Post-Doc

• University of Luxembourg, LU - Computational Cognitive Science and Modeling.

• Justus Liebig University, Giessen, DE - Visual neuroscience and neurostimulation.

• NeuroSpin, Saclay, FR - Mathematical concepts and their acquisition.

• University of Iceland in Reykjavik - PhD or Postdoc position at the Icelandic Vision Lab.

• Texas A&M University, US - Human states predictions (e.g., stress, learning, fatigue) and closed-loop technological mitigations in controlled and field environments using wearable neuro/physiological/behavioral sensors.

• Texas A&M University, US - Multimodal brain-behavior mappings of human-autonomy teaming across increasing contextual complexities. 

• Duke University, Durham, US - Neurocognitive mechanisms underpinning the regulation of cognitive stability and flexibility.

• Institute of Psychiatry and Neuroscience of Paris, FR - Memory and Perception.

• University of Milano-Bicocca, IT - The semantic side of novel word processing in adult speakers.

• Heinrich Heine University Düsseldorf, DE - Decision making and learning.

• Aix-Marseille University, Marseille, FR - Neural dynamics of auditory cognitive processes.

• UC Berkeley, US - Cognition and Action lab.

• Stem-cell and Brain Research institute, Lyon, FR - Ecological Cognition and Computation.

• Centre de Recherche de Cerveau et Cognition, Toulouse, FR - The role of travelling waves in cognition.

• Institute of Neuroscience, UC Louvain, BE - Brain stimulation to modulate pain perception in humans.

Other

• Assistant Professor in Cognitive Neuroscience - University of Groningen, NL

• Research Associate - University of Birmingham, UK.

• Associate in research - Duke University, Durham, US.

• Research Project Assistant, University of Dundee, SC - Auditory Brain Lab.

• Lecturer in Psychology, University of York, EN.

• RA, Chinese University of Hong Kong, CN.

• RA - Ernst Strüngman Institute, Frankfurt, DE.

---