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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. |
{{attachment:logo_line.gif}} |
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| == What you can do with BrainStorm == * Import MEG / EEG from the most popular file formats [[FileFormats|(list here)]] |
== News == <<HTML(<div style="margin-top: 0px; padding: 0px; border: 0px solid #999; float: right;"><A href="http://neuroimage.usc.edu/brainstorm/Jobs">)>> {{attachment:hiring.jpg||height="77",width="115"}} <<HTML(</A></div>)>> |
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| * Data visualization: * Various time series displays * Data mapping on the head surface * Generate slides and animations * Channel selection * Data filtering * 3D surface renderin |
<<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/all.js#xfbml=1"; fjs.parentNode.insertBefore(js, fjs);}(document, 'script', 'facebook-jssdk'));</script>)>> |
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| * 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 |
* '''Latest software updates''':<<BR>>[[News|http://neuroimage.usc.edu/brainstorm/News]] * '''New training opportunities''': [[Training|Register now!]]<<BR>>Montreal (March 16-20), Marseille (May), Seattle (Sept), Los Angeles (Oct) * '''Stay in touch with the Brainstorm community with'''''' [[http://www.facebook.com/BrainstormSoftware|Facebook]]'''<<BR>><<HTML(<div class="fb-like" data-href="http://www.facebook.com/BrainstormSoftware" data-send="true" data-width="450" data-show-faces="true"></div>)>> * <<HTML(<FORM METHOD="get" ACTION="http://neuroimage.usc.edu/bst/search_users.php" name="form" onSubmit="return validateForm(this);"><B>Find users by location</B>: <INPUT type='text' name='u' size=30><input type="submit" style="visibility: hidden;" /></FORM>)>> |
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| * Forward modeling: * Single sphere method * Overlapping spheres method * Realistic head models using BEM and FEM |
== Introduction == Brainstorm is a collaborative, open-source application dedicated to MEG/EEG/sEEG/ECoG data analysis (visualization, processing and advanced source modeling). |
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| * Group analysis: * Registration of individual brains on the MNI "Colin27" brain * Statistical analysis (t-tests, permutations) |
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. |
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| == What you cannot do with BrainStorm == * Pre-processing of the MEG/EEG recordings:<<BR>>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]]. |
Since the project started by the end of the 1990's, our server has registered more than 8,500 accounts and about 500 users are actively updating the software. See our [[Pub|reference page]] for a list of published studies featuring Brainstorm at work. |
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| == Requirements == !BrainStorm is written in Matlab code only, thus it can run on any operating system supported by Matlab (including Windows, Linux, MacOS...). |
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. |
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| If you have a Matlab licence: | 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="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! |
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| * You can download and run directly the BrainStorm source scripts, | . ''' {{attachment:brainstorm_banner.gif||height="209px",width="586px"}} ''' |
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| * Minimum Matlab version: '''7.1 (= R14-SP3)''' | == 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. |
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| If you do not have a Matlab licence: | 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. |
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| * 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 |
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]]) * Read data from the most popular file formats ([[#line-78|link]]) * Interactive access to data files in native formats ([[Tutorials/TutRawViewer|link]]) * Import data in Matlab * Import and order data in a well-organized database (by studies, subjects, conditions) * Review, edit, import, export event markers in continuous, ongoing recordings * Automatic detection of well-defined artifacts: eye blinks, heartbeats... ([[Tutorials/TutRawSsp|link]]) * Artifact correction using Signal Space Projections ([[Tutorials/TutRawSsp|SSP]]) * '''Pre-processing: ''' ([[Tutorials/TutRawAvg|link]]) * Epoching * Detection of bad trials / bad channels * Baseline correction * Frequency filtering * Resampling * Multiple options for epoch averaging ([[Tutorials/TutRawAvg|link]]) * Estimation of noise statistics for improved source modeling ([[Tutorials/TutNoiseCov|link]]) * '''Powerful and versatile visualization: ''' * Various time series displays ([[Tutorials/TutExploreRecodings|link]]) * Data mapping on 2D or 3D surfaces (disks, true geometry of sensor array, scalp surface, etc.) * Generate slides and animations (export as contact sheets, movies, jpegs, ...) * Flexible montage editor, channel selection and sensor clustering * '''MRI visualization and coregistration: ''' * Generate surfaces from MRI volume: head, inner skull and outer skull * Use individual or template anatomy (MNI / Colin27 or IBCM152 brain) * Template anatomy can be warped to individual head surface ([[Tutorials/TutWarping|link]]) * Import MRI volumes and tessellated surface envelopes ([[#line-78|link]]) * Automatic or interactive co-registration with the MEG/EEG coordinate system * Volume rendering (multiple display modes) * '''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/TutProcesses|link]]) * Automatic generation of scripts to perform full analysis ([[Tutorials/TutRawScript|link]]) * Flexible plug-in structure that makes the software easy to extend ([[Tutorials/TutUserProcess|link]]) * '''Head modeling: ''' ([[Tutorials/TutHeadModel|link]]) * MEG: Single sphere, overlapping spheres * EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG) * Interactive interface to define the best-fitting sphere * '''Source modeling: '''''' ''' ([[Tutorials/TutSourceEstimation|link]]) * L2 Minimum-norm current estimates * dSPM * sLORETA * All models can be cortically-constrained or not, and with/without constrained orientations * Dipole scanning ([[Tutorials/TutDipScan|link]]) * '''Source display and analysis: ''' * Multiple options for surface and volume rendering of the source maps * Re-projection of the sources in the MRI volume (from surface points to voxels) * Definition of regions of interest ([[Tutorials/TutScouts|scouts]]) * Projection of estimated sources on a surface with higher or lower resolution * Projection on a group template * Surface or volume spatial smoothing (for group analysis) * Share your results: screen captures, make movies and contact sheets! * Import and display of Neuromag's Xfit and CTF's DipoleFit dipole models ([[Tutorials/TutDipScan|link]]) * '''Time-frequency decompositions: ''' * Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transform and Hilbert transform ([[Tutorials/TutTimefreq|link]]) * Define time and frequency scales of interest * Multiple display modes available * '''Functional connectivity''': * Correlation, coherence, Granger causality, phase-locking value * 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 brain template (MNI/Colin27) * Statistical analysis (t-tests) * '''Documentation and support: ''' * Easy and automatic updates of the software * Detailed step-by-step [[Tutorials|tutorials]] for most common features * Active user forum supported by a large [[Community|user community]] == Supported file formats == === EEG: === * ANT EEProbe continuous (.cnt) * BDF / BDF+ (Biosemi 24bit binary) * BESA exports (.avr, .mul) * BrainVision BrainAmp (.eeg) * BrainVision Analyzer (.txt) * Cartool binary files (.ep, .eph) * Deltamed Coherence-Neurofile export (.txt/.bin) * EDF / EDF+ (European Data Format) * EEGLab sets (.set) * EGI NetStation epoch-marked file (.raw/.epoc) * MANSCAN Microamp (.mbi/.mb2) * Neuroscan (.cnt, .eeg, .avg, .dat) * NeuroScope (*.eeg;*.dat) * Any type of ASCII (text) files === MEG: === * CTF (.ds folders) * Elekta Neuromag FIFF (.fif) * BTi / 4D Neuroimaging * KRISS MEG (.kdf) * Yokogawa / KIT * LENA format === Sensors locations: === * ANT Xensor (.elc) * BESA (.sfp, .elp, .eps/.ela) * 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 === MRI volumes: === * Analyze (.img/.hdr) * BrainVISA GIS (.ima/.dim) * CTF (.mri) * MINC (.mnc) * MGH (.mgh, .mgz) * Neuromag (.fif) * Nifti-1 (.nii, .nii.gz) === 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 (tesselation is created automatically) === Surface atlases: === * BrainSuite (.dfs) * FreeSurfer (.annot, .label) * Gifti texture (.gii) === Dipole models: === * Elekta Neuromag XFit (.bdip) |
News
Latest software updates:
http://neuroimage.usc.edu/brainstorm/NewsNew training opportunities: Register now!
Montreal (March 16-20), Marseille (May), Seattle (Sept), Los Angeles (Oct)Stay in touch with the Brainstorm community with Facebook
Introduction
Brainstorm is a collaborative, open-source application dedicated to MEG/EEG/sEEG/ECoG data analysis (visualization, processing and advanced source modeling).
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.
Since the project started by the end of the 1990's, our server has registered more than 8,500 accounts and about 500 users are actively updating the software. 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)
Read data from the most popular file formats (link)
Interactive access to data files in native formats (?link)
- Import data in Matlab
- Import and order data in a well-organized database (by studies, subjects, conditions)
- Review, edit, import, export event markers in continuous, ongoing recordings
Automatic detection of well-defined artifacts: eye blinks, heartbeats... (?link)
Artifact correction using Signal Space Projections (?SSP)
Pre-processing: (?link)
Powerful and versatile visualization:
Various time series displays (?link)
- Data mapping on 2D or 3D surfaces (disks, true geometry of sensor array, scalp surface, etc.)
- Generate slides and animations (export as contact sheets, movies, jpegs, ...)
- Flexible montage editor, channel selection and sensor clustering
MRI visualization and coregistration:
- Generate surfaces from MRI volume: head, inner skull and outer skull
- Use individual or template anatomy (MNI / Colin27 or IBCM152 brain)
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
- Volume rendering (multiple display modes)
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:
Head modeling: (?link)
- MEG: Single sphere, overlapping spheres
- EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG)
- Interactive interface to define the best-fitting sphere
Source modeling: (?link)
- L2 Minimum-norm current estimates
- dSPM
- sLORETA
- All models can be cortically-constrained or not, and with/without constrained orientations
Dipole scanning (link)
Source display and analysis:
- Multiple options for surface and volume rendering of the source maps
- Re-projection of the sources in the MRI volume (from surface points to voxels)
Definition of regions of interest (?scouts)
- Projection of estimated sources on a surface with higher or lower resolution
- Projection on a group template
- Surface or volume spatial smoothing (for group analysis)
- Share your results: screen captures, make movies and contact sheets!
Import and display of Neuromag's Xfit and CTF's DipoleFit dipole models (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
- 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 brain template (MNI/Colin27)
- Statistical analysis (t-tests)
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
Supported file formats
EEG:
- ANT EEProbe continuous (.cnt)
- BDF / BDF+ (Biosemi 24bit binary)
- BESA exports (.avr, .mul)
BrainVision BrainAmp (.eeg)
BrainVision Analyzer (.txt)
- Cartool binary files (.ep, .eph)
- Deltamed Coherence-Neurofile export (.txt/.bin)
- EDF / EDF+ (European Data Format)
- EEGLab sets (.set)
EGI NetStation epoch-marked file (.raw/.epoc)
- MANSCAN Microamp (.mbi/.mb2)
- Neuroscan (.cnt, .eeg, .avg, .dat)
NeuroScope (*.eeg;*.dat)
- Any type of ASCII (text) files
MEG:
- CTF (.ds folders)
- Elekta Neuromag FIFF (.fif)
- BTi / 4D Neuroimaging
- KRISS MEG (.kdf)
- Yokogawa / KIT
- LENA format
Sensors locations:
- ANT Xensor (.elc)
- BESA (.sfp, .elp, .eps/.ela)
- 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
MRI volumes:
- Analyze (.img/.hdr)
- BrainVISA GIS (.ima/.dim)
- CTF (.mri)
- MINC (.mnc)
- MGH (.mgh, .mgz)
- Neuromag (.fif)
- Nifti-1 (.nii, .nii.gz)
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 (tesselation is created automatically)
Surface atlases:
BrainSuite (.dfs)
FreeSurfer (.annot, .label)
- Gifti texture (.gii)
Dipole models:
- Elekta Neuromag XFit (.bdip)