= Introduction =
Brainstorm is a collaborative open-source Matlab application dedicated to magnetoencephalography (MEG) and electroencephalography(EEG) data visualization, processing and cortical source estimation. <<BR>>Our intention is to make a comprehensive set of tools available to the scientific community involved in MEG/EEG experimental research.<<BR>>For physicians and researchers, the interest of this software package resides in its rich and intuitive graphic interface, which does not require any programming knowledge.

== 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

 * 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 a 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, permutations)

 * 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 ==
 * Intensive pre-processing of MEG/EEG recordings (noise cancelling, artifact correction/rejection, etc.):<<BR>> => use your constructor's software, or other software solutions (MNE, EEGLab, !FieldTrip, etc.). [[Links|See here]].

 * MRI segmentation:<<BR>> => use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]].

== 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: ===
 * CTF (.mri)
 * GIS (.ima/.dim) -- (brainVISA: {{http://brainvisa.info}} )
 * Analyze (.img/.hdr)
 * Nifti-1 (.nii)
 * Neuromag (.fif)
 * MGH (.mgh, .mgz)

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

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