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| Brainstorm is a free 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. | 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 (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 [[Download|downloadable package]]. Since the project started by the end of the 1990's, our server has registered more than 6,000 software downloads and about 500 users are actively updating the sofware. See our [[Pub|reference page]] for a list of published studies that have been using Brainstorm. Last but not least, Brainstorm is thoroughly documented in [[http://neuroimage.usc.edu/brainstorm3_register/download.php|these pages]] and support is provided through an [[http://neuroimage.usc.edu/forums|online forum]]. We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community! == 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 have an overview of the main features of the application. Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM (2011), ''Brainstorm: A User-Friendly Application for MEG/EEG Analysis'', '''Computational Intelligence and Neuroscience''', vol. 2011, Article ID 879716, 13 pages. doi:10.1155/2011/879716 [ [[http://www.hindawi.com/journals/cin/2011/879716/|html]], [[http://downloads.hindawi.com/journals/cin/2011/879716.pdf|pdf]] ] |
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| * Import MEG / EEG recordings from the most popular file formats ([[FileFormats|list here]]) | * 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) |
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| * Data visualization: | * 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 * Frequency filtering * 3D surface rendering |
* 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 |
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| * Graphical batching tools (apply a same process to many files in a few clicks) | * Graphical batching tools (apply the 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 |
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| * Minimum-norm imaging of the cortical current density | * 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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| * Statistical analysis (t-tests, permutations) | * 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 |
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| * Intensive pre-processing of MEG/EEG recordings (noise, artifact correction/rejection, re-averaging, etc.):<<BR>> => use your constructor's software, or other software solutions (MNE, EEGLab, etc.). [[Links|See here]]. | * MRI segmentation: Use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]]. |
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| * MRI segmentation:<<BR>> => use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]]. | * Advanced statistics: Use R, Statistica, SPSS, Matlab, Excel, etc. |
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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...). |
== 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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| If you have a Matlab licence: | === MEG: === * CTF (.ds directory) * Neuromag FIFF (.fif) * BTi / 4D Neuroimaging * LENA format |
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| * You can download and run directly the Brainstorm source scripts, * Minimum Matlab version: 7.1 (= R14-SP3) * Minimum Java VM version: 1.5 (To check that: type "ver" at Matlab command prompt) |
=== 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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| If you do not have a Matlab licence: | === MRI volumes: === * Analyze (.img/.hdr) * Nifti-1 (.nii) * CTF (.mri) * BrainVISA GIS (.ima/.dim) * Neuromag (.fif) * MGH (.mgh, .mgz) |
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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 |
=== Meshes: === * BrainVISA (.mesh) * !BrainSuite (.dsgl, .dfs) * !FreeSurfer * ASCII (.tri) * Neuromag (.fif) === Noise covariance matrix: === * Neuromag / MNE (.fif) * ASCII arrays === Dipoles: === * Elekta Neuromag XFit (.bdip) |
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 (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.
Since the project started by the end of the 1990's, our server has registered more than 6,000 software downloads and about 500 users are actively updating the sofware. See our reference page for a list of published studies that have been using Brainstorm.
Last but not least, Brainstorm is thoroughly documented in these pages and support is provided through an online forum.
We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community!
How to cite Brainstorm
Please cite the following reference in your publications if you have used our software for your data analyses:How to cite Brainstorm. It is also good offline reading to have an overview of the main features of the application.
Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM (2011), Brainstorm: A User-Friendly Application for MEG/EEG Analysis, Computational Intelligence and Neuroscience, vol. 2011, Article ID 879716, 13 pages. doi:10.1155/2011/879716 [ html, pdf ]
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
- 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 (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. ?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)