{{attachment:logo_line.gif}}

= Introduction =
Brainstorm is a collaborative, open-source application dedicated to magnetoencephalography (MEG) and electroencephalography(EEG) 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 to improve 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 [[Download|downloadable parckage]].

Last but not least, Brainstorm is thoroughly documented in [[Tutorials|these pages]] and support is provided through an [[http://neuroimage.usc.edu/forum|online forum]].

We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community!

== Reference paper ==
Please cite the following referenceBrainstorm reference paper in your publications if you have used our software for your analysis:[[CiteBrainstorm|How to cite Brainstorm]].

Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM, “Brainstorm: A User-Friendly Application for MEG/EEG Analysis,” Computational Intelligence and Neuroscience, vol. 2011, Article ID 879716, 13 pages, 2011. doi:10.1155/2011/879716 [ [[http://www.hindawi.com/journals/cin/2011/879716/|html]], [[http://downloads.hindawi.com/journals/cin/2011/879716.pdf|pdf]] ]



== What you can do with Brainstorm ==
 * MEG / EEG recordings:
  * Reading data from the most popular file formats ([[#line-78|list here]])
  * Interactive access to the original files, or copy in the database
  * Reviewing and editing of event markers in continuous files
  * Detecting automatically repetitive artifacts (eye blinks, heartbeats...)
  * Removing artifacts using Signal Space Projections (SSP)

 * Pre-processing:
  * Epoching
  * Detection of bad trials / bad channels
  * Baseline correction
  * Frequency filtering
  * Resampling
  * Averaging
  * Noise covariance estimation

 * Recordings visualization:
  * Various time series displays
  * Data mapping on 2D or 3D surfaces
  * Generate slides and animations
  * Channel selection, and manipulation of clusters of electrodes

 * MRI visualization and coregistration:
  * Analysis on individual anatomy or MNI / Colin27 brain
  * Import MRI and meshes from most of the existing file formats ([[#line-78|list here]])
  * Co-registration with the MEG/EEG coordinate system
  * Volume rendering (several display modes)
  * Deformation of the MNI template to fit an set of digitized head points

 * Database:
  * Classification of recordings with three levels of definition (protocol, subject, condition/event)
  * Quick access to all the data in a study
  * Quick comparison between subjects or conditions
  * Graphical batching tools (apply the same process to many files in a few clicks)

 * Forward modeling:
  * MEG: Single sphere, overlapping spheres
  * EEG: Berg's three-layer sphere
  * Interactive interface to define the best fitting sphere

 * Inverse modeling:
  * L2 Minimum-norm current estimates
  * dSPM
  * sLORETA
  * All methods can be cortically constrained or not, and with constrained orientations or not

 * Source display and analysis:
  * Surface and volume rendering of the estimated sources
  * Re-projection of the sources in the MRI volume
  * Definition of cortical regions of interest (scouts)
  * Re-projection of estimated sources on a surface with a higher or lower definition
  * Spatial smoothing before group analysis
  * Easy screen captures, creation of movies and contact sheets
  * Import and display of xfit dipoles
 * Time-frequency analysis:
  * Time-frequency decomposition of recordings and sources time series using Morlet wavelets
  * Time and frequency scales: linear or bands
  * Many display modes available

 * Group analysis:
  * Registration of individual brains on the MNI "Colin27" brain
  * Statistical analysis (t-tests)

 * Documentation and support:
  * Easy and automatic updates of the software
  * Detailed step by step tutorials for most of the common features
  * Active user forum

== What you cannot do with Brainstorm ==
 * MRI segmentation: Use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]].

 * Advanced statistics: Use R, Statistica, SPSS, Matlab, Excel, etc.

== Supported file formats ==
=== EEG: ===
 * EGI !NetStation epoch-marked file (.raw/.epoc)
 * Neuroscan (.cnt, .eeg, .avg, .dat)
 * !BrainAmp (.eeg)
 * EEGLab sets (.set)
 * Cartool simple binary files (.ep, .eph)
 * !ErpCenter (.erp/.hdr)
 * Any type of ASCII arrays

=== MEG: ===
 * CTF (.ds directory)
 * Neuromag FIFF (.fif)
 * BTi / 4D Neuroimaging
 * LENA format

=== Sensors locations: ===
 * Cartool (.xyz, .els)
 * BESA (.sfp, .elp, .eps/.ela)
 * Polhemus Isotrak (.pos, .elp)
 * Curry (.res, .rs3)
 * EEGLab (.ced, .xyz, .set)
 * EETrak (.elc)
 * EGI (.sfp)
 * EMSE (.elp)
 * Neuroscan (.dat, .tri)
 * ASCII arrays

=== MRI volumes: ===
 * Analyze (.img/.hdr)
 * Nifti-1 (.nii)
 * CTF (.mri)
 * BrainVISA GIS (.ima/.dim)
 * Neuromag (.fif)
 * MGH (.mgh, .mgz)

=== Meshes: ===
 * BrainVISA (.mesh)
 * !BrainSuite (.dsgl, .dfs)
 * !FreeSurfer
 * ASCII (.tri)
 * Neuromag (.fif)

=== Noise covariance matrix: ===
 * Neuromag / MNE (.fif)
 * ASCII arrays

=== Dipoles: ===
 * Elekta Neuromag XFit (.bdip)