Free software solutions for
MEG/EEG source imaging
François Tadel
Cognitive Neuroscience & Brain Imaging Lab., CNRS – University of Paris - Hôpital de la Salpêtrière Cognitive Neuroimaging Unit, Inserm U562 – NeuroSpin - CEA
I. Source imaging steps
II.
Software classification
III. BrainStorm demo
Pre-processing (EEG/MEG)
Source imaging Post-processing Pre-processing (MRI) Functional (EEG/MEG) Anatomy (MRI) Interpretation
Pre-processing (EEG/MEG)
• Basic but important processes:
– Artifact detection, rejection or reduction
– Noise reduction
– Bandpass filtering
– Averaging
– …
• Software solutions:
– Commercial packages (from MEG/EEG vendors or
3rd-party)
– Academic (free, open-source) solutions:
Pre-processing (MRI)
• Operations:
– Importation
– Segmentation of tissue envelopes
• scalp, skull, cortex (white vs. grey matter),
cerebellum…
– Surface meshes
• Dedicated academic software packages:
– BrainVISA / Anatomist, FreeSurfer,
BrainSuite, SPM, etc.
Source imaging
• Processes:
– Co-registration IRM – EEG/MEG
– Forward modelling
– Inverse estimation
• Software:
– BrainStorm
– MNE
– EEGlab
– FieldTrip
– LORETA
– NutMEG
Post-processing
• Operations:
– Inter-individual co-registration – Statistical analysis:
• exploration and inference
– Frequency-spectrum analysis and time-frequency decomposition
• Software:
– BrainStorm – MNE – EEGLab – FieldTrip – LORETA – NutMEGI.
Source imaging steps
II. Software classification
II. Software classification
• Modality : MEG and/or EEG
• Source model :
– Dipoles fitting or distributed sources
– Volume or surfaces
• Individual or template anatomy
• Interface:
– GUI or command line
– Database oriented or single analysis
– Interoperability with other systems
EEGLab
• MEG/EEG analysis:
– ERP segmentation, filtering, artifact rejection, averaging, … – ICA (Independent Component Analysis)
– Time/frequency analysis
• Source localization : dipole fitting only
• Interface:
– Nice graphical interface for visualization and computation – Possible to work on many subjects at the same time
• Software status:
– Matlab toolbox / work on all operating systems / Open source – Very popular : lots of plug-ins available
– Import most of the existing file formats
FieldTrip
• MEG/EEG analysis:
– ERP segmentation, filtering, artifact rejection, averaging, … – Advanced time/frequency analysis
• Source localization :
– Many forward and inverse models available (distributed and dipolar), on full MRI volume
– Many statistics and display tools, both on channels and sources
• Interface:
– Command line only : difficult to learn
– Users need to have a good programming experience
• Software status:
– Matlab toolbox / work on all operating systems / Open source – Import most of the existing file formats
Cartool
• EEG analysis:
– ERP segmentation, filtering, artifact rejection, averaging, … – Advanced time/frequency analysis
– Many statistical tools
– ERP segmentation in microstates
• Source localization :
– Computed by external programs, and visualized by Cartool
• Interface:
– Fast and beautiful MRI, EEG and sources visualization – Good interactivity, easy data exploration
• Software status:
– Free but not open source, C++, Windows only – Not widely distributed, but very stable
BrainVISA / Anatomist
• 3D/4D image processing:
– Automated and semi-automated pipelines for sMRI and fMRI processing
– Advanced MRI segmentation
– Extraction of head and cortical surfaces
• Source localization:
– Fully automated pipeline for EEG/MEG sources reconstruction – Based on BrainStorm algorithms
(distributed models, cortically constrained)
• Interface:
– Very rich visualization interface (Anatomist)
– Advanced database system: efficient classification of recordings – Adapted to process numerous subjects and conditions
– But not very interactive for EEG/MEG recordings and sources
• Software status:
BrainSuite
• Structural MRI :
– Automated extraction of head and cortical surfaces
– Extraction of skull (inner and outer surfaces)
– Results for surface reconstruction are better with
BrainVISA.
• Interface:
– Minimal visualization of MRI and surfaces
– Simple and fast
– 10 minutes to extract a cortex surface when using the
software for the first time
• Software status:
– C++/MFC, Windows only / Free but not open source
– Last update: June 2005…
FreeSurfer
• Structural MRI :
– Advanced MRI segmentation
– Automated extraction of head and cortical surfaces
– Good methods for inflation and normalization of
cortical surfaces
• Interface:
– GUI for surfaces and volumes visualization and
manipulations : useful but could be more interactive
– Computations from command line only.
• Software status:
– C / Linux, Solaris, IRIX, MacOSX / Open source
– Popular software : many users an developers
MNE
• MEG/EEG analysis:
– ERP segmentation, filtering, artifact rejection, averaging, …
• Source localization :
– Many forward models available
– Minimum norm estimator, cortically constrained – Possible to constrain source estimator with fMRI
• Interface:
– Everything accessible from the command line – Some features have a graphical interface
• Software status:
– Compiled C, Linux and MacOS/X
+ Matlab toolbox for reading Neuromag/FIF file format – Free but not open source
– Import most of the existing file formats – Linked with FreeSurfer
SPM5
• MEG/EEG analysis:
– ERP segmentation, filtering, artifact rejection, averaging, …
• Statistical analysis:
– Advanced statistical methods for fMRI processing
– Volume normalization (MNI or Talairach space) for group-based analysis
– Possibility to process EEG/MEG sources and fMRI in the same environment
• Source localization:
– Minimum norm estimator, not constrained – Sources in full MRI volume
• Interface:
– Graphical interface is poor and not interactive
• Software status:
– Matlab / work on all operating systems / Open source – Very popular : reference for fMRI statistical processing
LORETA
• Source localization:
– EEG only
– Minimum Laplacian estimator, not constrained
– Impossible to use individual anatomy
– Statistical methods on channels and sources
• Interface:
– Simple GUI, poor results
• Software status:
– Compiled executable / Windows only
BrainStorm
• Source localization:
– Many forward models available
– Many sources estimator available, all cortically constrained (minimum norm, beamformers, RAP-MUSIC)
– Statistical analysis on both channels and sources
– Minimalist surfaces normalization, for inter-subjects analysis
• Interface:
– Advanced and intuitive user interface for visualization, computation, and database manipulation
– Very interactive: best tool for data exploration – Database oriented : protocols/subjects/
• Software status:
– Matlab / work on all operating systems / Open source – Inter-operability: Imports files from EEGLab, FreeSurfer,
• Three or four independent steps:
– Pre-processing of MEG/EEG surface data
– Pre-processing of MRI (only if using individual anatomy) – Source estimation
– Post-processing of source dynamic maps
• Possible good combinations of software packages
• Examples:
– EEGLab + BrainVISA + BrainStorm (Matlab)
– Cartool + BrainSuite + BrainStorm + SPM (Windows) – FreeSurfer + MNE (Linux)
– EEGLab + FieldTrip (Matlab) – …
Commercial packages
• BESA
• ASA
• Curry
• EMSE
• BrainVoyager
• EEGLab:
Swartz Center for Computational Neuroscience University of California San Diego (US)
http://sccn.ucsd.edu/eeglab/ • FieldTrip:
F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen (NL)
http://www2.ru.nl/fcdonders/fieldtrip • Cartool:
D.Brunet, Functional Brain Mapping Laboratory University of Geneva (CH)
http://brainmapping.unige.ch/Cartool.htm • BrainVISA / Anatomist:
Various research groups around Paris (CNRS, INSERM, CEA) http://brainvisa.info
• BrainSuite:
DW. Shattuck, University of California Los Angeles and University of Southern California (US)
http://brainsuite.usc.edu/ • FreeSurfer:
Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital (US)
http://surfer.nmr.mgh.harvard.edu • MNE:
M.Hämäläinen, A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital (US)
www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php • SPM5:
Wellcome Trust Centre for Neuroimaging University College London (UK)
http://www.fil.ion.ucl.ac.uk/spm
• LORETA:
RD Pascual-Marqui, KEY Institute for Brain-Mind Research University of Zürich (CH)
http://www.uzh.ch/keyinst/NewLORETA • BrainStorm:
University of Southern California (US) Los Alamos National Laboratory (US) CNRS & INSERM, Paris (France)
http://neuroimage.usc.edu/brainstorm
