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| = Introduction = !BrainStorm is an integrated free Matlab toolbox dedicated to Magnetoencephalography(MEG) and Electroencephalography(EEG) data visualization and processing. Our intention is to make a comprehensive set of tools available to the scientific community involved in MEG/EEG experimental research. == What you can do with BrainStorm == * Import MEG / EEG from the most popular file formats [[FileFormats|(list here)]] * Data visualization: * Various time series displays * Data mapping on the head surface * Generate slides and animations * Channel selection * Data filtering * 3D surface renderin * MRI visualization and coregistration: * Import MRI scans, from most of the existing file formats ([[FileFormats|list here]]) * Co-registration with the MEG/EEG coordinate system * Volume rendering * Forward modeling: * Single sphere method * Overlapping spheres method * Realistic head models using BEM and FEM * Group analysis: * Registration of individual brains on the MNI "Colin27" brain * Statistical analysis (t-tests, permutations) == What you cannot do with BrainStorm == * Pre-processing of the MEG/EEG recordings:<<BR>> {1} use your constructor's software, or other software solutions (MNE, EEGLab, etc.). [[Links|See here]]. * MRI segmentation:<<BR>> => use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]]. == Requirements == !BrainStorm is written in Matlab code only, thus it can run on any operating system supported by Matlab (including Windows, Linux, MacOS...). If you have a Matlab licence: * You can download and run directly the !BrainStorm source scripts, * Minimum Matlab version: 7.1 (= R14-SP3) If you do not have a Matlab licence: * You can download the !BrainStorm binaries corresponding to your operating system. * The executables are build using the Matlab Compiler (mcc) * They will install automatically the Matlab Component Runtime (MCR) on your computer, a freely redistributable library |
{{attachment:logo_line.gif}} == News == <<HTML(<!-- div style="margin-top: -10px; padding: 0px; border: 0px solid #999; float: right; clear: right;"><A href="http://neuroimage.usc.edu/brainstorm/Jobs">)>> {{attachment:hiring.jpg||width="115",height="77"}} <<HTML(</A></div -->)>> <<HTML(<script async defer src="https://buttons.github.io/buttons.js"></script>)>> <<HTML(<div style="float: right;"><a class="github-button" href="https://github.com/brainstorm-tools/brainstorm3" data-style="mega" data-count-href="/brainstorm-tools/brainstorm3/stargazers" data-count-api="/repos/brainstorm-tools/brainstorm3#stargazers_count" data-count-aria-label="# stargazers on GitHub" aria-label="Star brainstorm-tools/brainstorm3 on GitHub">Star</a></div)>> <<HTML(<div id="fb-root"></div> <script>(function(d, s, id) {var js, fjs = d.getElementsByTagName(s)[0]; if (d.getElementById(id)) return; js = d.createElement(s); js.id = id;js.src = "//connect.facebook.net/en_US/sdk.js#xfbml=1&version=v2.5"; fjs.parentNode.insertBefore(js, fjs);}(document, 'script', 'facebook-jssdk'));</script>)>> <<HTML(<div style="float: right; clear: right; margin-top: 10px;" class="fb-like" data-href="http://www.facebook.com/BrainstormSoftware" data-layout="button_count" data-action="like" data-show-faces="true" data-share="false"></div>)>> <<HTML(<script language="javascript"> function searchforum() {window.open("https://www.google.com/search?q=" + document.getElementById('txtforum').value + "+site:http://neuroimage.usc.edu/forums", '_blank');}</script>)>> * '''New courses''': Beijing (April), Montreal/Quebec (May), Cambridge (June) - [[Training|Register]] * '''Software updates''': [[News|What's new]] | Follow us on [[http://www.facebook.com/BrainstormSoftware|Facebook]] and [[https://github.com/brainstorm-tools/brainstorm3|GitHub]] * <<HTML(<FORM METHOD="get" ACTION="http://neuroimage.usc.edu/bst/search_users.php" onSubmit="return validateForm(this);"><B>Find users by location</B>: <INPUT type='text' name='u' size=25 style="height: 22px; padding: 0px 10px 0px 10px;"></FORM>)>> * <<HTML(<FORM METHOD="get" onSubmit='searchforum(this); return false'><B>Search the user forum</B>: <INPUT type='text' id='txtforum' size=25 style="height: 22px; padding: 0px 10px 0px 10px;"></FORM>)>> == Introduction == Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: <<BR>>MEG, EEG, fNIRS, ECoG, depth electrodes and animal electrophysiology. Our objective is to share a comprehensive set of user-friendly tools with the scientific community using MEG/EEG as an experimental technique. For physicians and researchers, the main advantage of Brainstorm is its rich and intuitive graphic interface, which does not require any programming knowledge. We are also putting the emphasis on practical aspects of data analysis (e.g., with scripting for batch analysis and intuitive design of analysis pipelines) to promote reproducibility and productivity in MEG/EEG research. Finally, although Brainstorm is developed with Matlab (and Java), it does not require users to own a Matlab license: an executable, platform-independent (Windows, MacOS, Linux) version is made available in the downloadable package. To get an overview of the interface, you can watch this [[http://neuroimage.usc.edu/brainstorm/Screenshots|introduction video]]. Since the project started by the end of the 1990's, our server has registered more than 15,000 accounts. See our [[Pub|reference page]] for a list of published studies featuring Brainstorm at work. The best way to learn how to use Brainstorm, like any other academic software, is to benefit from local experts. However, you may be the first one in your institution to consider using Brainstorm for your research. We are happy to provide comprehensive [[Tutorials|online tutorials]] and support through our forum but there is nothing better than a course to make your learning curve steeper. Consult our [[Training|training pages]] for upcoming opportunities to learn better and faster. Finally, have a look regularly at our [[News|What's new]] page for staying on top of Brainstorm news and updates and <<HTML(<A href="https://www.facebook.com/brainstormsoftware">)>> ''' {{attachment:facebook_like.png|http://www.facebook.com/brainstormsoftware}} '''Like us on Facebook<<HTML(</A>)>> to stay in touch. We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community! . ''' {{attachment:brainstorm_banner.gif||width="586px",height="209px"}} ''' == Support == This software was generated primarily with support from the National Institutes of Health under grants 2R01-EB009048, R01-EB009048, R01-EB002010 and R01-EB000473. Primary support was provided by the Centre National de la Recherche Scientifique (CNRS, France) for the Cognitive Neuroscience & Brain Imaging Laboratory (La Salpetriere Hospital and Pierre & Marie Curie University, Paris, France), and by the Montreal Neurological Institute to the MEG Program at''' McGill '''University. Additional support was also from two grants from the French National Research Agency (ANR) to the Cognitive Neuroscience Unit (PI: Ghislaine Dehaene; Inserm/CEA, Neurospin, France) and to the ViMAGINE project (PI: Sylvain Baillet; ANR-08-BLAN-0250), and by the Epilepsy Center in the Cleveland Clinic Neurological Institute. == How to cite Brainstorm == Please cite the following reference in your publications if you have used our software for your data analyses:''' [[CiteBrainstorm|How to cite Brainstorm]].''' It is also good offline reading to get an overview of the main features of the application. Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM (2011)<<BR>>[[http://www.hindawi.com/journals/cin/2011/879716/|Brainstorm: A User-Friendly Application for MEG/EEG Analysis]]<<BR>>Computational Intelligence and Neuroscience, vol. 2011, ID 879716 == What you can do with Brainstorm == '''MEG/EEG recordings:''' * Digitize the position of the EEG electrodes and the subject's head shape | [[Tutorials/TutDigitize|link]] * Support for multiple modalities: [[Tutorials/Auditory|MEG]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG]], [[http://neuroimage.usc.edu/brainstorm/News#February_2015|sEEG]], [[http://neuroimage.usc.edu/brainstorm/News#February_2015|ECoG]], [[http://neuroimage.usc.edu/brainstorm/News#June_2015|animal LFP]], [[Tutorials/NIRSFingerTapping|NIRS]] * Read data from the most popular file formats | [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|link]] * Interactive access to data files in native formats | [[Tutorials/ReviewRaw|link]] * Import data in Matlab | [[http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Custom_processing|link]] * Import and order data in a well-organized database | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CreateProtocol#Database_structure|link]] * Review, edit and import event markers in continuous recordings | [[Tutorials/EventMarkers|link]] * Automatic detection of well-defined artifacts: eye blinks, heartbeats | [[Tutorials/ArtifactsDetect|link]] * Artifact correction: Signal Space Projections ([[Tutorials/ArtifactsSsp|SSP]]) * Independent Component Analysis ([[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Artifact_cleaning_with_ICA|ICA]]) * Detection of [[Tutorials/BadSegments|bad trials]] / [[Tutorials/BadChannels|bad channels]] * Baseline correction | [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epoching#Import_in_database|link]] * Power spectrum density | [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Evaluation_of_the_noise_level|link]] * Frequency filtering, resampling | [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Notch_filter|link]] * Epoching | [[Tutorials/Epoching|link]] * Averaging | [[Tutorials/Averaging|link]] '''Powerful and versatile visualization: ''' * Various time series displays | [[Tutorials/ReviewRaw|link]] * Data mapping on 2D or 3D surfaces | [[Tutorials/ExploreRecordings|link]] * Generate slides and animations (export as [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreRecordings#Contact_sheets|contact sheets]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreRecordings#Snapshots|snapshots]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreRecordings#Movie_studio|movies]], ...) * Flexible montage editor | [[Tutorials/MontageEditor|link]] * Channel selection and sensor clustering | [[Tutorials/ChannelClusters|link]] '''MRI visualization and coregistration: ''' * Generate surfaces from MRI volume: head, inner skull and outer skull | [[Tutorials/TutBem|link]] * Use individual or template anatomy (MNI / Colin27 or ICBM152 brain) | [[Tutorials/DefaultAnatomy|link]] * Template anatomy can be warped to individual head surface | [[Tutorials/TutWarping|link]] * Import MRI volumes and tessellated surface envelopes | [[Tutorials/ImportAnatomy|link]] * Automatic or interactive co-registration with the MEG/EEG coordinate system | [[Tutorials/ChannelFile|link]] * Volume rendering (multiple display modes) | [[Tutorials/ExploreAnatomy|link]] * Anatomical atlases: surface parcelations and sub-cortical regions | [[Tutorials/LabelFreeSurfer|link]] '''Database: Keep your data organized''' * Ordering of data by protocol, subject and condition/event * Quick access to all the data in a study for efficient, batch processing * Quick access to comparisons between subjects or conditions '''Graphical batching tools''': * Apply the same process to many files in a few clicks | [[Tutorials/PipelineEditor|link]] * Automatic generation of scripts to perform full analysis | [[Tutorials/Scripting|link]] * Flexible plug-in structure that makes the software easy to extend | [[Tutorials/TutUserProcess|link]] '''Head modeling: ''' * MEG: Single sphere, overlapping spheres | [[Tutorials/HeadModel|link]] * EEG: Berg's three-layer sphere, Boundary Element Models (with [[Tutorials/TutBem|OpenMEEG]]) * sEEG/ECoG: Boundary Element Models (with OpenMEEG) * Interactive interface to define the best-fitting sphere '''Source modeling: ''' * Estimation of noise statistics for improved source modeling | [[Tutorials/NoiseCovariance|link]] * L2 Minimum-norm current estimates | [[Tutorials/SourceEstimation|link]] * Normalizations: dSPM, sLORETA, Z-score | [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Source_map_normalization|link]] * All models can be cortically-constrained or not, and with/without constrained orientations * Dipole scanning | [[Tutorials/TutDipScan|link]] * Dipole fitting with FieldTrip | [[Tutorials/DipoleFitting|link]] * Import and display of Neuromag's Xfit and CTF's DipoleFit dipole models | [[Tutorials/TutDipScan|link]] * Simulation of MEG/EEG recordings from source activity | [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Model_evaluation|link]] '''Source display and analysis: ''' * Multiple options for surface and volume rendering of the source maps | [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Display:_Cortex_surface|link]] * Re-projection of the sources in the MRI volume (from surface points to voxels) * Definition of regions of interest | [[Tutorials/Scouts|link]] * Project the sources on a surface with higher or lower resolution | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|link]] * Project the sources on a group template | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|link]] * Surface or volume spatial smoothing | [[http://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup#Spatial_smoothing|link]] '''Time-frequency decompositions: ''' * Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transform and Hilbert transform | [[http://neuroimage.usc.edu/brainstorm/Tutorials/TimeFrequency|link]] * Define time and frequency scales of interest * Multiple display modes available '''Functional connectivity''': * Correlation, coherence, Granger causality, phase-locking value * Phase-amplitude coupling estimation * Both at sensor and source levels * Dynamic circle plots for representing dense and high-dimensional connectivity graphs '''Group analysis: ''' * Registration of individual brains to a template | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|link]] * Parametric and non-parametric statistics | [[Tutorials/Statistics|link]] * Standard group analysis pipeline | [[Tutorials/VisualSingle|single subject]] | [[Tutorials/VisualGroup|group]] * Guidelines for scripting the analysis of large datasets | [[http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#How_to_process_an_entire_study|link]] '''Documentation and support: ''' * Easy and automatic updates of the software * Detailed step-by-step [[Tutorials|tutorials]] for most common features * Active user [[http://neuroimage.usc.edu/forums/|forum]] supported by a large [[Community|user community]] * Organization of [[Training|training courses]] on demand == Supported file formats == <<HTML(<TABLE class="tuto-table"><TR><TD>)>> '''EEG / Electrophysiology''' * ANT EEProbe continuous (.cnt) * BDF / BDF+ (Biosemi 24bit binary) * BESA exports (.avr, .mul) * Blackrock NeuroPort (.nev, .nsX) * BrainVision BrainAmp (.eeg) * BrainVision Analyzer (.txt) * Cartool binary files (.ep, .eph) * Compumedics ProFusion Sleep (.rda) * Deltamed Coherence-Neurofile export (.txt/.bin) * EDF / EDF+ (European Data Format) * EEGLab sets (.set) * EGI NetStation epoch-marked file (.raw/.epoc) * FieldTrip structures (.mat) * g.tec / g.Recorder Matlab exports (.mat) * MANSCAN Microamp (.mbi/.mb2) * MEGA NeurOne (.bin) * Micromed (.trc) * Neuralynx (.ncs) * Neuroscan (.cnt, .eeg, .avg, .dat) * NeuroScope (.eeg;.dat) * Nihon Kohden (.EEG) * Any type of ASCII (text) files '''Dipole models''' * Elekta Neuromag XFit (.bdip) * CTF's DipoleFit (.dip) <<HTML(</TD><TD>)>> '''MEG''' * CTF (.ds folders) * Elekta Neuromag FIFF (.fif) * BTi / 4D Neuroimaging * KRISS MEG (.kdf) * BabyMEG system (.fif) * Yokogawa / KIT '''Other recordings''' * Brainsight NIRS (.nirs) * EyeLink eye tracker (.edf) '''Sensors locations''' * ANT Xensor (.elc) * BESA (.sfp, .elp, .eps/.ela) * BrainVision CapTrak (.bvct) * BrainVision electrode file (.bvef) * Cartool (.xyz, .els) * Curry (.res, .rs3) * EEGLab (.ced, .xyz, .set) * EETrak (.elc) * EGI (.sfp) * EMSE (.elp) * Neuroscan (.dat, .tri, .asc) * Polhemus (.pos .pol .elp .txt) * ASCII arrays <<HTML(</TD></TR><TR><TD>)>> '''MRI volumes''' * Analyze (.img/.hdr) * BrainVISA GIS (.ima/.dim) * CTF (.mri) * MINC (.mnc) * MGH (.mgh, .mgz) * Neuromag (.fif) * Nifti-1 (.nii, .nii.gz) '''Surface atlases''' * BrainSuite (.dfs) * FreeSurfer (.annot, .label) * Gifti texture (.gii) * SUMA atlas (.dset) <<HTML(</TD><TD>)>> '''Surface meshes''' * BrainVISA (.mesh) * BrainSuite (.dsgl, .dfs) * Curry BEM surfaces (.db*, .s0*) * FreeSurfer (lh.*, rh.*) * FSL: VTK (.vtk) * FSL: Geomview (.off) * MNI obj (.obj) * ASCII (.tri) * Neuromag (.fif) * 3D masks or atlases from MRI files <<HTML(</TD></TR></TABLE>)>> |
News
New courses: Beijing (April), Montreal/Quebec (May), Cambridge (June) - Register
Software updates: What's new | Follow us on Facebook and GitHub
Introduction
Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
MEG, EEG, fNIRS, ECoG, depth electrodes and animal electrophysiology.
Our objective is to share a comprehensive set of user-friendly tools with the scientific community using MEG/EEG as an experimental technique. For physicians and researchers, the main advantage of Brainstorm is its rich and intuitive graphic interface, which does not require any programming knowledge. We are also putting the emphasis on practical aspects of data analysis (e.g., with scripting for batch analysis and intuitive design of analysis pipelines) to promote reproducibility and productivity in MEG/EEG research. Finally, although Brainstorm is developed with Matlab (and Java), it does not require users to own a Matlab license: an executable, platform-independent (Windows, MacOS, Linux) version is made available in the downloadable package. To get an overview of the interface, you can watch this introduction video.
Since the project started by the end of the 1990's, our server has registered more than 15,000 accounts. See our reference page for a list of published studies featuring Brainstorm at work.
The best way to learn how to use Brainstorm, like any other academic software, is to benefit from local experts. However, you may be the first one in your institution to consider using Brainstorm for your research. We are happy to provide comprehensive online tutorials and support through our forum but there is nothing better than a course to make your learning curve steeper. Consult our training pages for upcoming opportunities to learn better and faster.
Finally, have a look regularly at our What's new page for staying on top of Brainstorm news and updates and 
Like us on Facebook to stay in touch. We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community!
Support
This software was generated primarily with support from the National Institutes of Health under grants 2R01-EB009048, R01-EB009048, R01-EB002010 and R01-EB000473.
Primary support was provided by the Centre National de la Recherche Scientifique (CNRS, France) for the Cognitive Neuroscience & Brain Imaging Laboratory (La Salpetriere Hospital and Pierre & Marie Curie University, Paris, France), and by the Montreal Neurological Institute to the MEG Program at McGill University.
Additional support was also from two grants from the French National Research Agency (ANR) to the Cognitive Neuroscience Unit (PI: Ghislaine Dehaene; Inserm/CEA, Neurospin, France) and to the ViMAGINE project (PI: Sylvain Baillet; ANR-08-BLAN-0250), and by the Epilepsy Center in the Cleveland Clinic Neurological Institute.
How to cite Brainstorm
Please cite the following reference in your publications if you have used our software for your data analyses: How to cite Brainstorm. It is also good offline reading to get an overview of the main features of the application.
Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM (2011)
Brainstorm: A User-Friendly Application for MEG/EEG Analysis
Computational Intelligence and Neuroscience, vol. 2011, ID 879716
What you can do with Brainstorm
MEG/EEG recordings:
Digitize the position of the EEG electrodes and the subject's head shape | link
Support for multiple modalities: MEG, EEG, sEEG, ECoG, animal LFP, NIRS
Read data from the most popular file formats | link
Interactive access to data files in native formats | link
Import data in Matlab | link
Import and order data in a well-organized database | link
Review, edit and import event markers in continuous recordings | link
Automatic detection of well-defined artifacts: eye blinks, heartbeats | link
Artifact correction: Signal Space Projections (SSP)
Independent Component Analysis (ICA)
Detection of bad trials / bad channels
Baseline correction | link
Power spectrum density | link
Frequency filtering, resampling | link
Epoching | link
Averaging | link
Powerful and versatile visualization:
Various time series displays | link
Data mapping on 2D or 3D surfaces | link
Generate slides and animations (export as contact sheets, snapshots, movies, ...)
Flexible montage editor | link
Channel selection and sensor clustering | link
MRI visualization and coregistration:
Generate surfaces from MRI volume: head, inner skull and outer skull | link
Use individual or template anatomy (MNI / Colin27 or ICBM152 brain) | link
Template anatomy can be warped to individual head surface | link
Import MRI volumes and tessellated surface envelopes | link
Automatic or interactive co-registration with the MEG/EEG coordinate system | link
Volume rendering (multiple display modes) | link
Anatomical atlases: surface parcelations and sub-cortical regions | link
Database: Keep your data organized
- Ordering of data by protocol, subject and condition/event
- Quick access to all the data in a study for efficient, batch processing
- Quick access to comparisons between subjects or conditions
Graphical batching tools:
Apply the same process to many files in a few clicks | link
Automatic generation of scripts to perform full analysis | link
Flexible plug-in structure that makes the software easy to extend | link
Head modeling:
MEG: Single sphere, overlapping spheres | link
EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG)
- sEEG/ECoG: Boundary Element Models (with OpenMEEG)
- Interactive interface to define the best-fitting sphere
Source modeling:
Estimation of noise statistics for improved source modeling | link
L2 Minimum-norm current estimates | link
Normalizations: dSPM, sLORETA, Z-score | link
- All models can be cortically-constrained or not, and with/without constrained orientations
Dipole scanning | link
Dipole fitting with FieldTrip | link
Import and display of Neuromag's Xfit and CTF's DipoleFit dipole models | link
Simulation of MEG/EEG recordings from source activity | link
Source display and analysis:
Multiple options for surface and volume rendering of the source maps | link
- Re-projection of the sources in the MRI volume (from surface points to voxels)
Definition of regions of interest | link
Project the sources on a surface with higher or lower resolution | link
Project the sources on a group template | link
Surface or volume spatial smoothing | link
Time-frequency decompositions:
Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transform and Hilbert transform | link
- Define time and frequency scales of interest
- Multiple display modes available
Functional connectivity:
- Correlation, coherence, Granger causality, phase-locking value
- Phase-amplitude coupling estimation
- Both at sensor and source levels
- Dynamic circle plots for representing dense and high-dimensional connectivity graphs
Group analysis:
Registration of individual brains to a template | link
Parametric and non-parametric statistics | link
Standard group analysis pipeline | single subject | group
Guidelines for scripting the analysis of large datasets | link
Documentation and support:
- Easy and automatic updates of the software
Detailed step-by-step tutorials for most common features
Active user forum supported by a large user community
Organization of training courses on demand
Supported file formats
| EEG / Electrophysiology
Dipole models
| MEG
Other recordings
Sensors locations
|
| MRI volumes
Surface atlases
| Surface meshes
|