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| = Introduction = 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. |
{{attachment:logo_line.gif}} == News == <<HTML(<div style="margin-top: 5px; padding: 0px; border: 0px solid #999; float: right; width:310px; "><TABLE Border=0 style="background-color: #f7f7f7;"><TR><TD colspan=2><A href="http://neuroimage.usc.edu/brainstorm/Training">New Brainstorm courses: Register now!</A></TD></TR><TR><TD><B>Montreal: </B></TD><TD>July 11, 2012</TD></TR><TR><TD><B>Paris: </B></TD><TD>August 31, 2012</TD></TR></TABLE></div>)>> * '''Latest software updates''' :<<BR>>[[News|http://neuroimage.usc.edu/brainstorm/News]] * '''Join the Brainstorm community now''' :<<BR>> [[http://www.facebook.com/BrainstormSoftware|facebook.com/BrainstormSoftware]] * '''Just announced:''' Full program information is now available for our [[BrainstormUserSymposiumParis2012|1st User Symposium]] and [[WorkshopBiomag2012|Training Session]] in Paris (Aug 31) and the [[UqamMegWorkshop|MEG and Software Workshop]] in Montreal (July 11). == About Brainstorm == . {{attachment:brainstorm_banner.gif||height="209px",width="586px"}} 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 7,000 accounts and about 500 users are actively updating the software. See our [[Pub|reference page]] for a list of published studies featuring Brainstorm at work! The best way to learn how to use Brainstorm, like any other academic software, is to benefit from local experts. However, you may be the first one in your institution to consider using Brainstorm for your research. We are happy to provide comprehensive online documentation and support throughour forum but there is nothing better than a course to make your learning curve steeper. Consult our [[Training|training pages]] for upcoming''' '''opportunities to learn better and faster! Finally, have a look regularly at our [[News|What's New]] pages for staying on top of Brainstorm news and updates and 'Like Us' on Facebook to stay in touch. [[http://www.facebook.com/brainstormsoftware|{{attachment:FBlike.png|http://www.facebook.com/brainstormsoftware}}]] We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community! == Support == This software was generated primarily with support from the '''National Institutes of Health''' under grants R01-EB002010, R01-EB009048, and R01-EB000473. Primary support was provided by the '''Centre National de la Recherche Scientifique''' (CNRS, France) for the Cognitive Neuroscience & Brain Imaging Laboratory (La Salpetriere Hospital and Pierre & Marie Curie University, Paris, France), and by the '''Montreal Neurological Institute''' to the MEG Program at McGill University. Additional support was also from two grants from the '''French National Research Agency''' (ANR) to the Cognitive Neuroscience Unit (PI: Ghislaine Dehaene; Inserm/CEA, Neurospin, France) and to the ViMAGINE project (PI: Sylvain Baillet; ANR-08-BLAN-0250), and by the Epilepsy Center in the Cleveland Clinic Neurological Institute. == 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 get 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:''' * Read data from the most popular file formats ([[#line-78|listed here]]) |
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| * Pre-processing: | * Interactive access to data files in native formats * Import data in Matlab * Import and order data in a well-organized database (by studies, subjects, conditions) * Review, edit, import, export event markers in continuous, ongoing recordings * Automatic detection of well-defined artifacts (eye blinks, heartbeats...) * Artifact correction using Signal Space Projections (SSP) * '''Pre-processing: ''' |
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| * Detection of bad trials / bad channels * Baseline correction * Frequency filtering * Resampling * Multiple options for epoch averaging * Estimation of noise statistics for improved source modeling |
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| * Averaging | * '''Powerful and versatile visualization: ''' * Various time series displays (epoched, continuous raw, butterfly, columns, etc.) * Data mapping on 2D or 3D surfaces (disks, true geometry of sensor array, scalp surface, etc.) * Generate slides and animations (export as contact sheets, movies, jpegs, ...) * Channel selection and sensor clustering (save and organize your favorites, share with your collaborators, etc.) |
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| * Frequency filtering | * '''MRI visualization and coregistration: ''' * Use individual or template anatomy (MNI / Colin27 brain) * Template anatomy can be warped to individual head surface * Import MRI volumes and tessellated surface envelopes from most of the existing file formats ([[#line-78|listed here]]) |
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| * Resampling | * Automatic or interactive co-registration with the MEG/EEG coordinate system * Volume rendering (multiple display modes) |
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| * Noise covariance estimation | * '''Database: Keep your data organized''' * Ordering of data, source models, time-frequency maps, statistical maps, etc. by protocol, subject and condition/event * Quick access to all the data in a study for efficient, batch processing * Quick access to comparisons between subjects or conditions * Graphical batching tools (apply the same process to many files e.g., your entire study, in a few clicks) |
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| * Manual definition of bad channels and bad epochs | * '''Head modeling: ''' * MEG: Single sphere, overlapping spheres * EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG) * Interactive interface to define the best-fitting sphere |
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| * Data visualization: * Various time series displays * Data mapping on flat surfaces or the head envelope * Generate slides and animations * Channel selection, and manipulation of clusters of electrodes * 3D surface rendering * MRI visualization and coregistration: * Analysis on individual anatomy or MNI / Colin27 brain. * Import MRI scans, from most of the existing file formats ([[FileFormats|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: * Single sphere method * Overlapping spheres method * Inverse modeling: * Minimum-norm imaging of the cortical current density |
* '''Source modeling: ''' * L2 Minimum-norm current estimates |
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| * All models can be cortically-constrained or not, and with/without constrained orientations | |
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| * Source display and analysis: * Surface rendering of the estimated sources |
* '''Source display and analysis: ''' * Multiple options for surface and volume rendering of the source maps * Re-projection of the sources in the MRI volume (from surface points to voxels) * Definition of regions of interest (scouts) * Re-projection of estimated sources on a surface with higher or lower resolution, on a group template * Surface or volume spatial smoothing (group analysis) * Share your results: screen captures, make movies and contact sheets! * Import and display of Xfit (MEG Elekta software) dipole models |
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| * Reprojection of the sources in the MRI volume | * '''Time-frequency decompositions: ''' * Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transfor, and Hilbert transform * Define time and frequency scales of interest * Multiple display modes available |
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| * Definition of cortical regions of interest (scouts) | * '''Group analysis: ''' * Registration of individual brains to a brain template (MNI/Colin27) * Statistical analysis (t-tests) |
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| * Reprojection of estimated sources on a surface with a higher or lower definition | * '''Documentation and support: ''' * Easy and automatic updates of the software * Detailed step-by-step [[Tutorials|tutorials]] for most common features |
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| * 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 |
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| == 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]]. |
== What you cannot do with Brainstorm (yet) == * 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. == Supported file formats == === EEG: === * ANT EEProbe continuous (.cnt) * BESA exports (.avr, .mul) * !BrainVision !BrainAmp (.eeg) * !BrainVision Analyzer (.txt) * Cartool binary files (.ep, .eph) * EDF / EDF+ * EEGLab sets (.set) * EGI !NetStation epoch-marked file (.raw/.epoc) * Neuroscan (.cnt, .eeg, .avg, .dat) * Any type of ASCII (text) files === MEG: === * CTF (.ds folders) * 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, .asc) * ASCII arrays === MRI volumes: === * Nifti-1 (.nii, .nii.gz) * Analyze (.img/.hdr) * BrainVISA GIS (.ima/.dim) * CTF (.mri) * MGH (.mgh, .mgz) * Neuromag (.fif) === Surface meshes: === * BrainVISA (.mesh) * !BrainSuite (.dsgl, .dfs) * !FreeSurfer * FSL: VTK (.vtk) * FSL: Geomview (.off) * ASCII (.tri) * Neuromag (.fif) === Noise statistics (sensor covariance arrays): === * Neuromag / MNE (.fif) * ASCII arrays === Dipole models: === * Elekta Neuromag XFit (.bdip) |
News
| New Brainstorm courses: Register now! | |
| Montreal: | July 11, 2012 |
| Paris: | August 31, 2012 |
Latest software updates :
http://neuroimage.usc.edu/brainstorm/NewsJoin the Brainstorm community now :
facebook.com/BrainstormSoftwareJust announced: Full program information is now available for our 1st User Symposium and Training Session in Paris (Aug 31) and the MEG and Software Workshop in Montreal (July 11).
About Brainstorm
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 7,000 accounts and about 500 users are actively updating the software. See our reference page for a list of published studies featuring Brainstorm at work!
The best way to learn how to use Brainstorm, like any other academic software, is to benefit from local experts. However, you may be the first one in your institution to consider using Brainstorm for your research. We are happy to provide comprehensive online documentation and support throughour forum but there is nothing better than a course to make your learning curve steeper. Consult our training pages for upcoming opportunities to learn better and faster!
Finally, have a look regularly at our What's New pages for staying on top of Brainstorm news and updates and 'Like Us' on Facebook to stay in touch. 
We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community!
Support
This software was generated primarily with support from the National Institutes of Health under grants R01-EB002010, R01-EB009048, and R01-EB000473.
Primary support was provided by the Centre National de la Recherche Scientifique (CNRS, France) for the Cognitive Neuroscience & Brain Imaging Laboratory (La Salpetriere Hospital and Pierre & Marie Curie University, Paris, France), and by the Montreal Neurological Institute to the MEG Program at McGill University.
Additional support was also from two grants from the French National Research Agency (ANR) to the Cognitive Neuroscience Unit (PI: Ghislaine Dehaene; Inserm/CEA, Neurospin, France) and to the ViMAGINE project (PI: Sylvain Baillet; ANR-08-BLAN-0250), and by the Epilepsy Center in the Cleveland Clinic Neurological Institute.
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 get 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:
Read data from the most popular file formats (listed here)
- Interactive access to data files in native formats
- Import data in Matlab
- Import and order data in a well-organized database (by studies, subjects, conditions)
- Review, edit, import, export event markers in continuous, ongoing recordings
- Automatic detection of well-defined artifacts (eye blinks, heartbeats...)
- Artifact correction using Signal Space Projections (SSP)
Pre-processing:
- Epoching
- Detection of bad trials / bad channels
- Baseline correction
- Frequency filtering
- Resampling
- Multiple options for epoch averaging
- Estimation of noise statistics for improved source modeling
Powerful and versatile visualization:
- Various time series displays (epoched, continuous raw, butterfly, columns, etc.)
- Data mapping on 2D or 3D surfaces (disks, true geometry of sensor array, scalp surface, etc.)
- Generate slides and animations (export as contact sheets, movies, jpegs, ...)
- Channel selection and sensor clustering (save and organize your favorites, share with your collaborators, etc.)
MRI visualization and coregistration:
- Use individual or template anatomy (MNI / Colin27 brain)
- Template anatomy can be warped to individual head surface
Import MRI volumes and tessellated surface envelopes from most of the existing file formats (listed here)
- Automatic or interactive co-registration with the MEG/EEG coordinate system
- Volume rendering (multiple display modes)
Database: Keep your data organized
- Ordering of data, source models, time-frequency maps, statistical maps, etc. by protocol, subject and condition/event
- Quick access to all the data in a study for efficient, batch processing
- Quick access to comparisons between subjects or conditions
- Graphical batching tools (apply the same process to many files e.g., your entire study, in a few clicks)
Head modeling:
- MEG: Single sphere, overlapping spheres
- EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG)
- Interactive interface to define the best-fitting sphere
Source modeling:
- L2 Minimum-norm current estimates
- dSPM
- sLORETA
- All models can be cortically-constrained or not, and with/without constrained orientations
Source display and analysis:
- Multiple options for surface and volume rendering of the source maps
- Re-projection of the sources in the MRI volume (from surface points to voxels)
- Definition of regions of interest (scouts)
- Re-projection of estimated sources on a surface with higher or lower resolution, on a group template
- Surface or volume spatial smoothing (group analysis)
- Share your results: screen captures, make movies and contact sheets!
- Import and display of Xfit (MEG Elekta software) dipole models
Time-frequency decompositions:
- Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transfor, and Hilbert transform
- Define time and frequency scales of interest
- Multiple display modes available
Group analysis:
- Registration of individual brains to a brain template (MNI/Colin27)
- Statistical analysis (t-tests)
Documentation and support:
- Easy and automatic updates of the software
Detailed step-by-step tutorials for most common features
- Active user forum
What you cannot do with Brainstorm (yet)
MRI segmentation: Use FreeSurfer, BrainSuite or BrainVisa. ?See here.
- Advanced statistics: Use R, Statistica, SPSS, Matlab, Excel, etc.
Supported file formats
EEG:
- ANT EEProbe continuous (.cnt)
- BESA exports (.avr, .mul)
BrainVision BrainAmp (.eeg)
BrainVision Analyzer (.txt)
- Cartool binary files (.ep, .eph)
- EDF / EDF+
- EEGLab sets (.set)
EGI NetStation epoch-marked file (.raw/.epoc)
- Neuroscan (.cnt, .eeg, .avg, .dat)
- Any type of ASCII (text) files
MEG:
- CTF (.ds folders)
- 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, .asc)
- ASCII arrays
MRI volumes:
- Nifti-1 (.nii, .nii.gz)
- Analyze (.img/.hdr)
- BrainVISA GIS (.ima/.dim)
- CTF (.mri)
- MGH (.mgh, .mgz)
- Neuromag (.fif)
Surface meshes:
- BrainVISA (.mesh)
BrainSuite (.dsgl, .dfs)
FreeSurfer
- FSL: VTK (.vtk)
- FSL: Geomview (.off)
- ASCII (.tri)
- Neuromag (.fif)
Noise statistics (sensor covariance arrays):
- Neuromag / MNE (.fif)
- ASCII arrays
Dipole models:
- Elekta Neuromag XFit (.bdip)