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| == Introduction == ---- <<BR>> |
{{attachment:logo_line.gif}} |
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| !BrainStorm is an integrated free Matlab toolkit 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 = 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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| ---- '''BrainStorm features include:''''''[[BrainStorm/brainstorm/TutorialImportCTFData.html]]''' |
== Reference paper == 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]] ] |
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| * [[BrainStorm/brainstorm/TutorialVisualizeData.html|Translation routines to get the user data into the BrainStorm database - Import filters include translators of]][[http://www.ctf.com/|CTF Systems Inc.]], and soon, [[http://www.neuromag.com/|Neuromag]] and [[http://www.biomagtech.com/index.html|BTi]] data formats (contributions are welcome); | Please cite Brainstorm reference paper in your publications if you have used our software for your analysis:[[CiteBrainstorm|How to cite Brainstorm]]. |
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| * '''[[BrainStorm/brainstorm/TutorialVisualizeData.html|Data visualization tools]]''': Various time series displays; Data mapping on the head surface; Generate slides and animations; Channel selection; Data filtering, 3D Surface rendering * '''[[BrainStorm/brainstorm/TutorialImportMRIData.html|MRI visualization and co-registration]]''': Import MRI scans, co-registration with the MEG/EEG coordinate system; Superimpose MEG/EEG sources and f-MRI analyze results to the MRI ; Volume rendering; Scalp segmentation * '''[[BrainStorm/brainstorm/TutorialHeadModel.html|Forward modeling]] '''includes the single sphere and the overlapping sphere approaches ; realistic head models using BEM and FEM ('''new''') * '''[[BrainStorm/brainstorm/TutorialMinNorm.html|Inverse modeling]] '''features the RAP-MUSIC approach using current dipole models but also 1st-order multipole models of the primary neural current sources. Models for synchronous pairs of sources are also |
== 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) |
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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: |
* Pre-processing: * Epoching * Detection of bad trials / bad channels * Baseline correction * Frequency filtering * Resampling * Averaging * Noise covariance estimation |
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| * You can download and run directly the BrainStorm source scripts, * Minimum Matlab version: '''7.1 (= R14-SP3)''' |
* 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 |
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| If you do not have a Matlab licence: | * 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 |
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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 |
* 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 == * 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) |
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.
Reference paper
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 [ html, pdf ]
Please cite Brainstorm reference paper in your publications if you have used our software for your analysis:How to cite Brainstorm.
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 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
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)