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| == Introduction == ---- !BrainStorm is an integrated free Matlab toolbox dedicated to '''Magnetoencephalography''' (MEG) and '''Electroencephalography''' (EEG) data visualization and processing. Our intention is to make a comprehensive set of tools available to the scientific community involved in MEG/EEG experimental research. |
= Introduction = ||<tablewidth="100%">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. || {{attachment:logo.gif||height="158px",width="262px"}} || |
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| === What you can do with BrainStorm === * Import MEG / EEG from the most popular file formats [[FileFormats|(list here)]] * Data visualization: |
== 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: |
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| * Data mapping on the head surface | * Data mapping on 2D or 3D surfaces |
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| * Channel selection * Data filtering * 3D surface renderin |
* Channel selection, and manipulation of clusters of electrodes |
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| * Import MRI scans, from most of the existing file formats ([[FileFormats|list here]]) | * Analysis on individual anatomy or MNI / Colin27 brain * Import MRI and meshes from most of the existing file formats ([[#line-78|list here]]) |
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| * Volume rendering | * 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) |
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| * Single sphere method * Overlapping spheres method * Realistic head models using BEM and FEM |
* 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 |
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| === What you cannot do with BrainStorm === * Pre-processing of the MEG/EEG recordings:<<BR>>use your constructor's software, or other software solutions (MNE, EEGLab, etc.). [[Links|See here]]. |
* Documentation and support: * Easy and automatic updates of the software * Detailed step by step tutorials for most of the common features * Active user forum |
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| * MRI segmentation:<<BR>>use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]]. | == 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]]. |
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| <<BR>> | * MRI segmentation:<<BR>> => use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]]. |
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| == Requirements == ---- !BrainStorm is written in Matlab code only, thus it can run on any operating system supported by Matlab (including Windows, Linux, MacOS...). If you have a Matlab licence: |
== 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 |
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| * You can download and run directly the BrainStorm source scripts, * Minimum Matlab version: '''7.1 (= R14-SP3)''' |
=== MEG: === * CTF (.ds directory) * Neuromag FIFF (.fif) * BTi / 4D Neuroimaging * LENA format |
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| If you do not have a Matlab licence: | === 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 |
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| * You can download the BrainStorm binaries corresponding to your operating system. * The executables are build using the Matlab Compiler (mcc) * They will install automatically the Matlab Component Runtime (MCR) on your computer, a freely redistributable library |
=== 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 |
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. |
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![[ATTACH]](/brainstorm/Introduction?action=AttachFile&do=upload_form&ticket=006726443b.6e60691569e036afa6f0122440e817551d22f06e&target=logo.gif "[ATTACH]"){kind=small}
What you can do with Brainstorm
- MEG / EEG recordings:
Reading data from the most popular file formats (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 (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.). ?See here.MRI segmentation:
=> use FreeSurfer, BrainSuite or BrainVisa. ?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:
)
- 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