= Introduction =
Brainstorm is a collaborative open-source Matlab application dedicated to magnetoencephalography (MEG) and electroencephalography(EEG) data visualization, processing and cortical source estimation. <
>Our intention is to make a comprehensive set of tools available to the scientific community involved in MEG/EEG experimental research.<
>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.):<
> => use your constructor's software, or other software solutions (MNE, EEGLab, !FieldTrip, etc.). [[Links|See here]].
* MRI segmentation:<
> => 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