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| <<HTML(<div style="margin-top: -10px; 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>)>> <<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=v2.3"; fjs.parentNode.insertBefore(js, fjs);}(document, 'script', 'facebook-jssdk'));</script>)>> * '''Latest software updates and bug fixes''':<<BR>>[[News|http://neuroimage.usc.edu/brainstorm/News]] * '''New training opportunities''': [[Training|Register now!]]<<BR>>Seattle (Sept 30), Los Angeles (Oct 26-27), Grenoble (December), Geneva (December) * '''Stay in touch, follow us on'''''' [[http://www.facebook.com/BrainstormSoftware|Facebook]]''' <<HTML(<div class="fb-like" data-href="http://www.facebook.com/BrainstormSoftware" data-layout="button_count" data-action="like" data-show-faces="false" data-share="false" style="float: right; margin-top: -15px; margin-right: 15px;"></div>)>> * <<HTML(<FORM METHOD="get" ACTION="http://neuroimage.usc.edu/bst/search_users.php" name="form" onSubmit="return validateForm(this);"><B>Connect with users around you: enter the name of your city/institution</B>: <INPUT type='text' name='u' size=30><input type="submit" style="visibility: hidden;" /></FORM>)>> |
<<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||height="77",width="115"}} <<HTML(</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: 20px;" class="fb-like" data-href="http://www.facebook.com/BrainstormSoftware" data-layout="button_count" data-action="like" data-show-faces="true" data-share="true"></div>)>> * '''New courses''': Montreal (Nov 7-11), San Diego (Nov 10) - [[Training|Register now]] * '''New positions''': Research assistant in Montreal - [[Jobs|Apply now]] * '''Software updates''': [[News|What's new]] | Follow us on [[http://www.facebook.com/BrainstormSoftware|Facebook]] * <<HTML(<FORM METHOD="get" ACTION="http://neuroimage.usc.edu/bst/search_users.php" name="form" onSubmit="return validateForm(this);"><B>Connect with users around you</B>: Enter the name of your city/institution: <INPUT type='text' name='u' size=30><input type="submit" style="visibility: hidden;" /></FORM>)>> |
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| Brainstorm is a collaborative, open-source application dedicated to MEG/EEG/sEEG/ECoG data analysis (visualization, processing and advanced source modeling). | Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: <<BR>>MEG, EEG, fNIRS, ECoG, depth electrodes and animal electrophysiology. |
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| Since the project started by the end of the 1990's, our server has registered more than 10,000 accounts. See our [[Pub|reference page]] for a list of published studies featuring Brainstorm at work. | Since the project started by the end of the 1990's, our server has registered more than 13,000 accounts. See our [[Pub|reference page]] for a list of published studies featuring Brainstorm at work. |
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| 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! | 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! |
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| * Digitize the position of the EEG electrodes and the subject's head shape ([[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|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]]) |
* 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 ([[http://Tutorials/ArtifactsSsp|SSP]]) and 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]] |
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| * 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 |
* 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]] |
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| * 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) |
* 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 | [[http://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]] |
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| * 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) |
* 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) |
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| * '''Source modeling: '''''' ''' ([[Tutorials/TutSourceEstimation|link]]) * L2 Minimum-norm current estimates * dSPM * sLORETA |
* '''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]] |
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| * Dipole scanning ([[Tutorials/TutDipScan|link]]) | * Dipole scanning | [[Tutorials/TutDipScan|link]] * Dipole fitting with FieldTrip | [[Tutorials/DipoleFitting|link]] * Simulation of MEG/EEG recordings from source activity | [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Model_evaluation|link]] |
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| * Multiple options for surface and volume rendering of the source maps | * Multiple options for surface and volume rendering of the source maps | |
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| * Phase-amplitude coupling estimation | |
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| * Registration of individual brains to a brain template (MNI/Colin27) * Statistical analysis (t-tests) |
* Registration of individual brains to a template | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|link]] * Parametric and non-parametric statistics | [[Tutorials/Statistics|link]] * Guidelines for scripting the analysis of large datasets | [[http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#How_to_process_an_entire_study|link]] |
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| === EEG: === | === EEG / Electrophysiology: === |
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| * Blackrock NeuroPort (.nev, .nsX) | |
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| * FieldTrip structures (.mat) * g.tec / g.Recorder Matlab exports (.mat) |
|
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| * MEGA NeurOne (.bin) * Neuralynx (.ncs) |
|
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| * BabyMEG system (.fif) | |
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| * LENA format | === Other recordings: === * EyeLink eye tracker (.edf) |
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| * BrainVision CapTrak (.bvct) * BrainVision electrode file (.bvef) |
|
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| * 3D masks or atlases from MRI files (tesselation is created automatically) | * 3D masks or atlases from MRI files (tesselation is automatically created) |
News
New courses: Montreal (Nov 7-11), San Diego (Nov 10) - Register now
New positions: Research assistant in Montreal - Apply now
Software updates: What's new | Follow us on Facebook
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 13,000 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) and Independent Component Analysis (ICA)
* Detection of bad trials / bad channels
Powerful and versatile visualization:
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:
Head modeling:
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
Simulation of MEG/EEG recordings from source activity | 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
- Phase-amplitude coupling estimation
- Both at sensor and source levels
- Dynamic circle plots for representing dense and high-dimensional connectivity graphs
Group analysis:
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 / 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)
- Neuralynx (.ncs)
- 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)
- BabyMEG system (.fif)
- Yokogawa / KIT
Other recordings:
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
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 automatically created)
Surface atlases:
BrainSuite (.dfs)
FreeSurfer (.annot, .label)
- Gifti texture (.gii)
- SUMA atlas (.dset)
Dipole models:
- Elekta Neuromag XFit (.bdip)