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== 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 17,500 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!

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== 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 ==
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'''EEG / Electrophysiology'''

 * ANT EEProbe continuous (.cnt)
 * ANT ASA (.msm/.msr)
 * BDF / BDF+ (Biosemi 24bit binary)
 * BESA exports (.avr, .mul)
 * Blackrock NeuroPort (.nev, .nsX)
 * BrainVision BrainAmp (.eeg)
 * BrainVision Analyzer (.txt)
 * Cartool binary files (.ep, .eph)
 * CED Spike2 (.smr)
 * Compumedics ProFusion Sleep (.rda)
 * Deltamed Coherence-Neurofile export (.txt/.bin)
 * EDF / EDF+ (European Data Format)
 * EEGLab sets (.set)
 * ERPLab results (.erp)
 * 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)
 * Nicolet (.e)
 * Nihon Kohden (.EEG)
 * Ripple Trellis (.nev, .nsX)
 * Any type of ASCII (text) files

'''Dipole models'''

 * Elekta Neuromag XFit (.bdip)
 * CTF's DipoleFit (.dip)

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'''MEG'''

 * CTF (.ds folders)
 * Elekta Neuromag FIFF (.fif)
 * BTi / 4D Neuroimaging
 * KRISS MEG (.kdf)
 * BabyMEG system (.fif)
 * Yokogawa / KIT
 * MEG-BIDS formatted databases

'''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

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'''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)

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'''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

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