|
Size: 12048
Comment:
|
Size: 19243
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
| <<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">Next Brainstorm course moved to larger venue: Register now!</A></TD></TR><TR><TD><B>Paris: </B></TD><TD>August 31, 2012</TD></TR></TABLE></div -->)>> <<HTML(<!-- div style="margin-top: 0px; padding: 0px; border: 0px solid #999; float: right; width:220px; "><a href="http://www.facebook.com/media/set/?set=a.287879241316067.56071.117589778345015&type=3"><img align="right" alt="Biomag 2012" class="attachment" src="/brainstorm/Introduction?action=AttachFile&do=get&target=ParisBrainstormCourse_small.jpg" title="Biomag 2012" /></a></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]] * '''New training opportunities ''': Halifax (Fev 16) and Seattle (Jun 21)<<BR>>[[Training|Register to those workshops]] * '''Importand update for the user of Brainstorm-generated scripts''':<<BR>>[[Note2013Jan22|You may have to update your scripts, read more...]] |
<<HTML(<!-- div style="margin-top: -10px; padding: 0px; border: 0px solid #999; float: right; clear: right;"><A href="http://neuroimage.usc.edu/brainstorm/Jobs">)>> {{attachment:hiring.jpg||height="77",width="115"}} <<HTML(</A></div -->)>> <<HTML(<script async defer src="https://buttons.github.io/buttons.js"></script>)>> <<HTML(<div style="float: right;"><a class="github-button" href="https://github.com/brainstorm-tools/brainstorm3" data-style="mega" data-count-href="/brainstorm-tools/brainstorm3/stargazers" data-count-api="/repos/brainstorm-tools/brainstorm3#stargazers_count" data-count-aria-label="# stargazers on GitHub" aria-label="Star brainstorm-tools/brainstorm3 on GitHub">Star</a></div)>> <<HTML(<div id="fb-root"></div> <script>(function(d, s, id) {var js, fjs = d.getElementsByTagName(s)[0]; if (d.getElementById(id)) return; js = d.createElement(s); js.id = id;js.src = "//connect.facebook.net/en_US/sdk.js#xfbml=1&version=v2.5"; fjs.parentNode.insertBefore(js, fjs);}(document, 'script', 'facebook-jssdk'));</script>)>> <<HTML(<div style="float: right; clear: right; margin-top: 5px; margin-right:-3px;" class="fb-like" data-href="http://www.facebook.com/BrainstormSoftware" data-layout="button_count" data-action="like" data-show-faces="true" data-share="false"></div>)>> <<HTML(<script async defer src="https://platform.twitter.com/widgets.js"></script>)>> <<HTML(<div style="float: right; clear: right;"><a href="https://twitter.com/brainstorm2day?ref_src=twsrc%5Etfw" class="twitter-follow-button" data-show-count="false">Follow @brainstorm2day</a></div>)>> <<HTML(<script language="javascript"> function searchforum() {window.open("https://www.google.com/search?q=" + document.getElementById('txtforum').value + "+site:http://neuroimage.usc.edu/forums", '_blank');}</script>)>> <<HTML(<!--)>> * '''New courses''': CuttingEEG / Aix-en-Provence: October 4th - [[https://neuroimage.usc.edu/brainstorm/WorkshopAix2021|Program]] <<HTML(-->)>> * '''Problems with automatic updates''': [[https://github.com/brainstorm-tools/brainstorm3/issues/308#issuecomment-646026943|Solution #1]] | [[https://neuroimage.usc.edu/forums/t/undefined-function-icon-y-up-iconloader/35737|Solution #2]] * '''Software updates''': [[News|What's new]] | [[http://www.facebook.com/BrainstormSoftware|Facebook]] | [[https://twitter.com/brainstorm2day|Twitter]] | [[https://github.com/brainstorm-tools/brainstorm3|GitHub]] * <<HTML(<FORM METHOD="get" ACTION="http://neuroimage.usc.edu/bst/search_users.php" onSubmit="return validateForm(this);"><B>Find users by location</B>: <INPUT type='text' name='u' size=25 style="height: 22px; padding: 0px 10px 0px 10px;"></FORM>)>> |
| Line 14: | Line 33: |
| 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 8,000 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 [[Tutorials|online tutorials]] and support through our 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]]''' '''page for staying on top of Brainstorm news and updates and <<HTML(<A href="www.facebook.com/brainstormsoftware">)>> ''' {{attachment:facebook_like.png|http://www.facebook.com/brainstormsoftware}} '''Like us on Facebook<<HTML(</A>)>> to stay in touch.''' '''We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community! '' '' |
Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: <<BR>>MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology. Our objective is to share a comprehensive set of user-friendly tools with the scientific community using MEG/EEG as an experimental technique. For clinician-scientists and researchers, the main advantage of Brainstorm is its easy 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. To get an overview of the interface, you can watch this [[http://neuroimage.usc.edu/brainstorm/Screenshots|introduction video]]. Since the project started by the end of the 1990's, our server has registered [[Community|more than 38,000 users]], contributing thousands of scientific publications. 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 [[Tutorials|online tutorials]] and support through our 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]] page for staying on top of Brainstorm news and updates and <<HTML(<A href="https://www.facebook.com/brainstormsoftware">)>> ''' {{attachment:facebook_like.png|http://www.facebook.com/brainstormsoftware}} '''Like us on Facebook<<HTML(</A>)>> to stay in touch. We hope you enjoy using Brainstorm as much as we enjoy developing and sharing these tools with the community! <<BR>> <<HTML(<center><iframe id="ytplayer" type="text/html" width="640" height="360" src="https://www.youtube.com/embed/30eFJUrRcN4?autoplay=0&origin=https://neuroimage.usc.edu/brainstorm" frameborder="0"></iframe></center>)>> <<HTML(<!-- )>> |
| Line 26: | Line 51: |
| <<HTML( -->)>> |
|
| Line 27: | Line 54: |
| 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. '' '' |
This software was generated primarily with support from the National Institutes of Health under grants R01-EB026299, 2R01-EB009048, R01-EB009048, R01-EB002010 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. |
| Line 34: | Line 61: |
| 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]] ] ''''' ''''' |
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)<<BR>>[[http://www.hindawi.com/journals/cin/2011/879716/|Brainstorm: A User-Friendly Application for MEG/EEG Analysis]]<<BR>>Computational Intelligence and Neuroscience, vol. 2011, ID 879716 |
| Line 39: | Line 66: |
| * '''MEG/EEG recordings:''' ''''' ''''' * Digitize the position of the EEG electrodes and the subject's head shape using a Polhemus device ''''' ''''' * Read data from the most popular file formats ([[#line-78|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: ''' ''''' ''''' * Generate surfaces from MRI volume: head, inner skull and outer skull * 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]]) ''''' ''''' * 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 ''''' ''''' * '''Functional connectivity''': * Correlation, coherence, Granger causality, phase-locking value * Both at sensor and source levels * Dynamic circle plots for representing dense and high-dimensional connectivity graphs * '''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|tutorials]] for most common features ''''' ''''' * Active user forum ''''' ''''' |
'''MEG/EEG recordings''' * Digitize the position of the EEG electrodes and the subject's head shape | [[Tutorials/TutDigitize|link]] * Support for multiple modalities | [[Tutorials/Auditory|MEG]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity|sEEG]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|ECoG]], [[Tutorials/NIRSFingerTapping|NIRS]], [[https://neuroimage.usc.edu/brainstorm/e-phys/Introduction|electrophysiology]] * Read data from the most popular file formats | [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|link]] * Interactive access to data files in native formats | [[Tutorials/ReviewRaw|link]] * Import data in Matlab | [[http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Custom_processing|link]] * Import and order data in a well-organized database | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CreateProtocol#Database_structure|link]] * Review, edit and import event markers in continuous recordings | [[Tutorials/EventMarkers|link]] * Automatic detection of well-defined artifacts: eye blinks, heartbeats | [[Tutorials/ArtifactsDetect|link]] * Artifact correction: Signal Space Projections ([[Tutorials/ArtifactsSsp|SSP]]) * Independent Component Analysis ([[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Artifact_cleaning_with_ICA|ICA]]) * Detection of [[Tutorials/BadSegments|bad trials]] / [[Tutorials/BadChannels|bad channels]] * Baseline correction | [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epoching#Import_in_database|link]] * Power spectrum density | [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Evaluation_of_the_noise_level|link]] * Frequency filtering, resampling | [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Notch_filter|link]] * Epoching | [[Tutorials/Epoching|link]] * Averaging | [[Tutorials/Averaging|link]] '''Powerful and versatile visualization ''' * Various time series displays | [[Tutorials/ReviewRaw|link]] * Data mapping on 2D or 3D surfaces | [[Tutorials/ExploreRecordings|link]] * Generate slides and animations (export as [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreRecordings#Contact_sheets|contact sheets]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreRecordings#Snapshots|snapshots]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreRecordings#Movie_studio|movies]], ...) * Flexible montage editor | [[Tutorials/MontageEditor|link]] * Channel selection and sensor clustering | [[Tutorials/ChannelClusters|link]] '''MRI visualization and coregistration ''' * Import individual MRI volumes and surfaces | [[Tutorials/ImportAnatomy|link]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer|FreeSurfer]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite|BrainSuite]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa|BrainVISA]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET|CIVET]] * Deface MRI images | [[https://neuroimage.usc.edu/brainstorm/News#March_2019|link]] * Normalize MRI to MNI space | [[https://neuroimage.usc.edu/brainstorm/CoordinateSystems#MNI_coordinates|link]] * Use anatomy templates | [[Tutorials/DefaultAnatomy|link]] * Warp templates to individual head surface | [[Tutorials/TutWarping|link]] * Generate surfaces from MRI volume | [[https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#Anatomy_folder|head]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutBem|skull]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Generate_default_surfaces|cortex]] * Automatic or interactive co-registration with the MEG/EEG coordinate system | [[Tutorials/ChannelFile|link]] * Volume rendering (multiple display modes) | [[Tutorials/ExploreAnatomy|link]] * Anatomical atlases: surface parcelations and sub-cortical regions | [[Tutorials/LabelFreeSurfer|link]] '''Database: Keep your data organized''' * Ordering of data 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 in a few clicks | [[Tutorials/PipelineEditor|link]] * Automatic generation of scripts to perform full analysis | [[Tutorials/Scripting|link]] * Flexible plug-in structure that makes the software easy to extend | [[Tutorials/TutUserProcess|link]] '''Head modeling ''' * MEG: Single sphere, overlapping spheres | [[Tutorials/HeadModel|link]] * EEG: Berg's three-layer sphere, Boundary Element Models (with [[Tutorials/TutBem|OpenMEEG]]) and the Finite Element Models (with [[https://neuroimage.usc.edu/brainstorm/https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro|DUNEuro]]) * sEEG/ECoG: Boundary Element Models (with OpenMEEG) and the Finite Element Models (with [[https://neuroimage.usc.edu/brainstorm/https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro|DUNEuro]]) * Interactive interface to define the best-fitting sphere '''Source modeling ''' * Estimation of noise statistics for improved source modeling | [[Tutorials/NoiseCovariance|link]] * L2 Minimum-norm current estimates | [[Tutorials/SourceEstimation|link]] * Normalizations: dSPM, sLORETA, Z-score | [[https://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Standardization_of_source_maps|link]] * All models can be cortically-constrained or not, and with/without constrained orientations * Source estimation on [[https://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Display:_Cortex_surface|cortical surface]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource|MRI volume]] or [[http://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas|sub-cortical atlases]] * Dipole scanning | [[Tutorials/TutDipScan|link]] * Dipole fitting with FieldTrip | [[Tutorials/DipoleFitting|link]] * Import and display of Neuromag's Xfit and CTF's DipoleFit dipole models | [[Tutorials/TutDipScan|link]] * Simulation of MEG/EEG recordings from source activity | [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Model_evaluation|link]] '''Source display and analysis ''' * Multiple options for surface and volume rendering of the source maps | [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Display:_Cortex_surface|link]] * Re-projection of the sources in the MRI volume (from surface points to voxels) * Definition of regions of interest | [[Tutorials/Scouts|link]] * Project the sources on a surface with higher or lower resolution | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|link]] * Project the sources on a group template | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|link]] * Surface or volume spatial smoothing | [[http://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup#Spatial_smoothing|link]] '''Time-frequency decompositions ''' * Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transform and Hilbert transform | [[http://neuroimage.usc.edu/brainstorm/Tutorials/TimeFrequency|link]] * Define time and frequency scales of interest * Multiple display modes available '''Functional connectivity''' * Correlation, coherence, Granger causality, phase-locking value | [[https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity|link]] * Phase-amplitude coupling estimation | [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutPac|link]] * Both at sensor and source levels * Dynamic circle plots for representing dense and high-dimensional connectivity graphs * Representation of functional connectivity on anatomical fibers | [[https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity|link]] '''Machine learning''' * Decoding / Multivariate pattern analysis with SVM or LDA | [[https://neuroimage.usc.edu/brainstorm/Tutorials/Decoding|link]] '''Group analysis ''' * Registration of individual brains to a template | [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|link]] * Parametric and non-parametric statistics | [[Tutorials/Statistics|link]] * Standard group analysis pipeline | [[Tutorials/VisualSingle|single subject,]] [[Tutorials/VisualGroup|group]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/Workflows|roadmaps]] * Guidelines for scripting the analysis of large datasets | [[http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#How_to_process_an_entire_study|link]] '''Documentation and support ''' * Easy and automatic updates of the software * Detailed step-by-step [[Tutorials|tutorials]] for most common features * Active user [[http://neuroimage.usc.edu/forums/|forum]] supported by a large [[Community|user community]] * Organization of [[Training|training courses]] on demand |
| Line 120: | Line 180: |
| === EEG: === * ANT EEProbe continuous (.cnt) ''''' ''''' * BDF / BDF+ (Biosemi 24bit binary) ''''' ''''' * BESA exports (.avr, .mul) ''''' ''''' * !BrainVision !BrainAmp (.eeg) ''''' ''''' * !BrainVision Analyzer (.txt) ''''' ''''' * Cartool binary files (.ep, .eph) ''''' ''''' * EDF / EDF+ (European Data Format) ''''' ''''' * EEGLab sets (.set) ''''' ''''' * EGI !NetStation epoch-marked file (.raw/.epoc) ''''' ''''' * MANSCAN Microamp (.mbi/.mb2) ''''' ''''' * 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) ''''' ''''' |
<<HTML(<TABLE class="tuto-table"><TR><TD>)>> '''EEG / Electrophysiology''' * ADInstruments LabChart (.adicht) * ANT ASA (.msm/.msr) * ANT EEProbe (.cnt, .avr) * Axion AxIS (.raw) * BCI2000 (.dat) * BDF / BDF+ (Biosemi 24bit binary) * BESA exports (.avr, .mul) * BIDS-formatted datasets * BIOPAC AcqKnowledge (.acq) * Blackrock NeuroPort (.nev, .nsX) * BrainVision BrainAmp (.eeg) * BrainVision Analyzer (.txt) * Cartool binary files (.ep, .eph) * CED Spike2 (.smr, .smrx, .son) * Compumedics ProFusion Sleep (.rda) * Curry 6-7 (.dat/.dap/rs3) * Curry 8 (.cdt/.dpa) * Deltamed Coherence-Neurofile export (.txt/.bin) * EDF / EDF+ (European Data Format) * EEGLab sets (.set) * ERPLab results (.erp) * EGI NetStation epoch-marked file (.raw/.epoc) * EGI-Philips (.mff) * EmotivPRO (.edf) * FieldTrip structures (.mat) * g.tec / g.Recorder (.mat, .hdf5) * Intan (.rhd, .rhs) * MANSCAN Microamp (.mbi/.mb2) * Matlab matrix (.mat) * MEGA NeurOne (.bin) * Micromed (.trc) * Muse (.csv) * Neuralynx (.ncs) * Neurodata Without Borders (.nwb) * Neuroelectrics (.easy, .nedf) * NeurOne (.bin) * Neuroscan (.cnt, .eeg, .avg, .dat) * NeuroScope (.eeg, .dat) * Nicolet (.e) * Nihon Kohden (.EEG) * Open Ephys flat binary (*.dat) * Plexon (.plx, .pl2) * Ripple Trellis (.nev, .nsX) * The Virtual Brain (.h5) * Tucker Davis Technologies (.tdt) * Wearable Sensing (.csv) * Any type of ASCII (text) files '''Data structures of similar applications''' * EEGLAB * FieldTrip * MNE-Python * SPM12 '''Dipole models''' * Elekta Neuromag XFit (.bdip) * CTF's DipoleFit (.dip) '''Surface atlases''' * BrainSuite (.dfs) * FreeSurfer (.annot, .label) * Gifti texture (.gii) * SUMA atlas (.dset) <<HTML(</TD><TD>)>> '''MEG''' * CTF (.ds folders) * Elekta Neuromag FIFF (.fif) * BTi / 4D Neuroimaging * KRISS MEG (.kdf) * BabyMEG system (.fif) * Ricoh MEG (.sqd, .con, .raw, .ave) * Yokogawa / KIT (.sqd, .con, .raw, .ave) * York Instruments MEGSCAN (.meghdf5) * MEG-BIDS formatted databases '''fNIRS''' * Brainsight NIRS (.nirs) * SNIRF (.snirf) '''Other recordings''' * EyeLink eye tracker (.edf) * Tobii Pro Glasses (.tsv) '''Sensors locations''' * ANT Xensor (.elc) * BESA (.sfp, .elp, .eps/.ela) * BrainVision CapTrak (.bvct) * BrainVision electrode file (.bvef) * Cartool (.xyz, .els) * Curry (.res, .rs3) * EEGLab (.ced, .xyz, .set) * EETrak (.elc) * EGI (.sfp) * EMSE (.elp) * Localite (.csv) * Neuroscan (.dat, .tri, .asc) * Polhemus (.pos .pol .elp .txt) * SimNIBS (.csv) * ASCII arrays '''MRI volumes''' * Analyze (.img/.hdr) * BrainVISA GIS (.ima/.dim) * CTF (.mri) * DICOM (using SPM converter) * MINC (.mnc) * MGH (.mgh, .mgz) * Neuromag (.fif) * Nifti-1 (.nii, .nii.gz) '''Surface meshes''' * ASCII (.tri) * BrainVISA (.mesh) * BrainSuite (.dsgl, .dfs) |
| Line 164: | Line 310: |
| * !FreeSurfer (lh.*, rh.*)''''' ''''' * FSL: VTK (.vtk) ''''' ''''' * FSL: Geomview (.off) ''''' ''''' * ASCII (.tri) ''''' ''''' * Neuromag (.fif) ''''' ''''' * 3D masks or atlases from MRI files (tesselation is created automatically) === Surface atlases: === * !FreeSurfer (.annot, .label) * Gifti texture (.gii) === Noise statistics (sensor covariance arrays): === * Neuromag / MNE (.fif) ''''' ''''' * ASCII arrays ''''' ''''' === Dipole models: === * Elekta Neuromag XFit (.bdip) ''''' ''''' |
* FreeSurfer (lh.*, rh.*) * FSL: VTK (.vtk) * FSL: Geomview (.off) * MNI obj (.obj) * Neuromag (.fif) * SimNIBS/Gmsh (.msh) * 3D masks or atlases from MRI files <<HTML(</TD></TR></TABLE>)>> |
News
Problems with automatic updates: Solution #1 | Solution #2
Software updates: What's new | Facebook | Twitter | GitHub
Introduction
Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.
Our objective is to share a comprehensive set of user-friendly tools with the scientific community using MEG/EEG as an experimental technique. For clinician-scientists and researchers, the main advantage of Brainstorm is its easy 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. To get an overview of the interface, you can watch this introduction video.
Since the project started by the end of the 1990's, our server has registered more than 38,000 users, contributing thousands of scientific publications. 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 tutorials and support through our 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 page 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-EB026299, 2R01-EB009048, R01-EB009048, R01-EB002010 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, ID 879716
What you can do with Brainstorm
MEG/EEG recordings
Digitize the position of the EEG electrodes and the subject's head shape | link
Support for multiple modalities | MEG, EEG, sEEG, ECoG, NIRS, electrophysiology
Read data from the most popular file formats | link
Interactive access to data files in native formats | link
Import data in Matlab | link
Import and order data in a well-organized database | link
Review, edit and import event markers in continuous recordings | link
Automatic detection of well-defined artifacts: eye blinks, heartbeats | link
Artifact correction: Signal Space Projections (SSP)
Independent Component Analysis (ICA)
Detection of bad trials / bad channels
Baseline correction | link
Power spectrum density | link
Frequency filtering, resampling | link
Epoching | link
Averaging | link
Powerful and versatile visualization
Various time series displays | link
Data mapping on 2D or 3D surfaces | link
Generate slides and animations (export as contact sheets, snapshots, movies, ...)
Flexible montage editor | link
Channel selection and sensor clustering | link
MRI visualization and coregistration
Import individual MRI volumes and surfaces | link, FreeSurfer, BrainSuite, BrainVISA, CAT, CIVET
Deface MRI images | link
Normalize MRI to MNI space | link
Use anatomy templates | link
Warp templates to individual head surface | link
Automatic or interactive co-registration with the MEG/EEG coordinate system | link
Volume rendering (multiple display modes) | link
Anatomical atlases: surface parcelations and sub-cortical regions | link
Database: Keep your data organized
- Ordering of data 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 in a few clicks | link
Automatic generation of scripts to perform full analysis | link
Flexible plug-in structure that makes the software easy to extend | link
Head modeling
MEG: Single sphere, overlapping spheres | link
EEG: Berg's three-layer sphere, Boundary Element Models (with OpenMEEG) and the Finite Element Models (with DUNEuro)
sEEG/ECoG: Boundary Element Models (with OpenMEEG) and the Finite Element Models (with DUNEuro)
- Interactive interface to define the best-fitting sphere
Source modeling
Estimation of noise statistics for improved source modeling | link
L2 Minimum-norm current estimates | link
Normalizations: dSPM, sLORETA, Z-score | link
- All models can be cortically-constrained or not, and with/without constrained orientations
Source estimation on cortical surface, MRI volume or sub-cortical atlases
Dipole scanning | link
Dipole fitting with FieldTrip | link
Import and display of Neuromag's Xfit and CTF's DipoleFit dipole models | link
Simulation of MEG/EEG recordings from source activity | link
Source display and analysis
Multiple options for surface and volume rendering of the source maps | link
- Re-projection of the sources in the MRI volume (from surface points to voxels)
Definition of regions of interest | link
Project the sources on a surface with higher or lower resolution | link
Project the sources on a group template | link
Surface or volume spatial smoothing | link
Time-frequency decompositions
Time-frequency analyses of sensor data and sources time series using Morlet wavelet, Fast Fourier Transform and Hilbert transform | link
- Define time and frequency scales of interest
- Multiple display modes available
Functional connectivity
Correlation, coherence, Granger causality, phase-locking value | link
Phase-amplitude coupling estimation | link
- Both at sensor and source levels
- Dynamic circle plots for representing dense and high-dimensional connectivity graphs
Representation of functional connectivity on anatomical fibers | link
Machine learning
Decoding / Multivariate pattern analysis with SVM or LDA | link
Group analysis
Registration of individual brains to a template | link
Parametric and non-parametric statistics | link
Standard group analysis pipeline | single subject, group, roadmaps
Guidelines for scripting the analysis of large datasets | link
Documentation and support
- Easy and automatic updates of the software
Detailed step-by-step tutorials for most common features
Active user forum supported by a large user community
Organization of training courses on demand
Supported file formats
| EEG / Electrophysiology
Data structures of similar applications
Dipole models
Surface atlases
| MEG
fNIRS
Other recordings
Sensors locations
MRI volumes
Surface meshes
|