Diff for "Introduction"

Differences between revisions 198 and 721 (spanning 523 versions)

News

Next courses:
Boys Town, Nebraska (USA): Oct 9-11, 2024 Program
Los Angeles, California (USA): Dec 5, 2024 Program
Problems with automatic updates: Solutions #1 and #2
Software updates: News | Facebook | Twitter | GitHub | Linkedin
Find users by location:

Introduction

Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology. The application is free; a Matlab license is not required to use it.

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.

We are happy to provide comprehensive documentation via online tutorials and data, and support through a user forum to help you learn how to use Brainstorm. We also deliver in-person and online courses: consult our training pages for upcoming opportunities to learn to use Brainstorm better and faster.

Finally, browse the 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
Generate surfaces from MRI volume | head, skull, cortex
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

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)

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)
Curry BEM surfaces (.db*, .s0*)
FreeSurfer (lh.*, rh.*)
FSL: VTK (.vtk)
FSL: Geomview (.off)
MNI obj (.obj)
Neuromag (.fif)
SimNIBS/Gmsh (.msh)
3D masks or atlases from MRI files

Development, release and distribution

Brainstorm follows a continuous development and release model. Brainstorm is updated on a rolling basis to ensure that users have access to the latest features, improvements and bug fixes as soon as they are ready. These updates are regularly published on the Brainstorm GitHub repository, and the version in the download page are updated everyday.

Updates can be obtained:

Automatically: at the Brainstorm startup, the user gets notified for updates and can download a new version is necessary.
Manually: this is be started within the GUI with the menu Update > Update Brainstorm
GitHub: for users and developers experienced in git and GitHub, latest Brainstorm source code can be retrieved from the Brainstorm GitHub repository.

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-<<HTML(<BR><div style="background-color: #eeeeff; margin: 15px; padding: 10px; border: 1px solid #999;"><B><U>Just Announced: New Brainstorm Courses</U></B><BR><BR><B>Date : </B>Saturday, April 28, 2012<BR><B>Location : </B>McGovern Institute for Brain Research, MIT, Boston, USA<BR><B>Program and registration: </B>TBA</div><BR>)>>More information on upcoming training sessions at: [[http://www.facebook.com/BrainstormSoftware|facebook.com/BrainstormSoftware]]

= Welcome! =
Brainstorm is a collaborative, open-source application dedicated to  magnetoencephalography (MEG) and electroencephalography(EEG) data  analysis ('''visualization, processing and advanced source modeling''').

{{attachment:brainstorm_banner.gif}}

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 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 [[http://neuroimage.usc.edu/brainstorm/Tutorials|online documentation]] and support through[[http://neuroimage.usc.edu/forums|our forum]] but there is nothing better than a [[Training|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[[http://www.facebook.com/brainstormsoftware|'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!
+== News ==
<<HTML(<div style="margin-top: -10px; padding: 0px; border: 0px solid #999; float: right; clear: right;"> <A href="http://neuroimage.usc.edu/brainstorm/Jobs">)>>

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<<HTML(<div style="float:  left;margin-right: 10px;"><a href="https://neuroimage.usc.edu/brainstorm/Jobs"><img alt="hiring.jpg" class="attachment" height="77" src="/brainstorm/Introduction?action=AttachFile&amp;do=get&amp;target=hiring.jpg" title="hiring.jpg" width="120"></a></div)>>

<<HTML(<div style="float:  right; clear: right; margin-top: 5px; margin-right:-3px;"><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 async defer crossorigin="anonymous" src="https://connect.facebook.net/en_US/sdk.js#xfbml=1&version=v18.0" nonce="JgAfk5ol"></script>)>>

<<HTML(<div onclick="location.href='https://www.facebook.com/BrainstormSoftware';" style="position: relative; float:  right; clear: right; margin-top: 5px; margin-right:-3px; cursor: pointer;"><div 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><div style="position: absolute; top:0; left:0;width: 100%;height: 100%;"><p>&nbsp;</p></div></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>)>>

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<<HTML(<div style="float: right; clear: right;"><div class="g-ytsubscribe" data-channelid="UCPXmMBgSZCRgfKBDtHKb77Q" data-layout="default" data-count="default"></div></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(<!--)>>

<<HTML(-->)>>

 * '''Next courses''':

 . Boys Town, Nebraska (USA): '''Oct 9-11, 2024''' [[https://neuroimage.usc.edu/brainstorm/WorkshopBoysTown2024|Program]]

 .

 . Los Angeles, California (USA): '''Dec 5, 2024''' [[https://neuroimage.usc.edu/brainstorm/WorkshopLA2024|Program]]

 * '''Problems with automatic updates''': Solutions [[https://github.com/brainstorm-tools/brainstorm3/issues/308#issuecomment-646026943|#1]] and [[https://neuroimage.usc.edu/forums/t/undefined-function-icon-y-up-iconloader/35737|#2]]

 * '''Software updates''': [[News]] | [[http://www.facebook.com/BrainstormSoftware|Facebook]] | [[https://twitter.com/brainstorm2day|Twitter]] | [[https://github.com/brainstorm-tools/brainstorm3|GitHub]] | [[https://www.linkedin.com/company/brainstorm-neuroimage|Linkedin]]

 * <<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>)>>

== Introduction ==
Brainstorm is a collaborative, open-source application dedicated to the analysis       of brain recordings: <<BR>>MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology. The application is free; a Matlab license is not required to use it.

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 [[Pub|thousands of scientific publications]].

We are happy  to provide comprehensive documentation via [[Tutorials|online tutorials]] and data, and support through [[https://neuroimage.usc.edu/forums/|a user forum]] to help you learn how to use Brainstorm. We also deliver in-person and online courses: consult our [[Training|training pages]] for upcoming opportunities to learn to use Brainstorm better and faster.

Finally, browse the [[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(<!-- )>>

 . ''' {{attachment:brainstorm_banner.gif||height="209px",width="586px"}} '''

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== 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 [[https://www.mcgill.ca/bic/meg-unit|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.
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-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
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- * '''MEG/EEG recordings:'''
  * Read data from the most popular file formats ([[#line-78|listed here]]); can import from multiple ASCII files as well

  * 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 ([[#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 wavelets
  * 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|tutorials]] for most common features

  * Active user forum

== What you cannot do with Brainstorm (yet) ==
 * MRI segmentation: Use !FreeSurfer, !BrainSuite or !BrainVisa. [[Links|See here]].

 * Advanced statistics: Use R, Statistica, SPSS, Matlab, Excel, etc.
+'''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 106:
+Line 199:
-=== EEG: ===
+<<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)
-Line 108:
+Line 210:
- * !BrainAmp (.eeg)
+ * BIDS-formatted datasets
 * BIOPAC AcqKnowledge (.acq)
 * Blackrock NeuroPort (.nev, .nsX)
 * BrainVision BrainAmp (.eeg)
 * BrainVision Analyzer (.txt)
-Line 110:
+Line 216:
- * EDF / EDF+
+ * 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)
-Line 112:
+Line 223:
- * EGI !NetStation epoch-marked file (.raw/.epoc)
+ * 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)
-Line 114:
+Line 240:
+ * 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)
-Line 116:
+Line 251:
-=== MEG: ===
+'''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'''
-Line 118:
+Line 275:
- * Neuromag FIFF (.fif)
+ * Elekta Neuromag FIFF (.fif)
-Line 120:
+Line 277:
- * LENA format

=== Sensors locations: ===
+ * 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)
-Line 124:
+Line 301:
- * BESA (.sfp, .elp, .eps/.ela)
 * Polhemus Isotrak (.pos, .elp)
-Line 131:
+Line 306:
+ * Localite (.csv)
-Line 132:
+Line 308:
+ * Polhemus (.pos .pol .elp .txt)
 * SimNIBS (.csv)
-Line 134:
+Line 312:
-=== MRI volumes: ===
 * Nifti-1 (.nii, .nii.gz)
+'''MRI volumes'''
-Line 139:
+Line 317:
+ * DICOM (using SPM converter)
 * MINC (.mnc)
-Line 141:
+Line 321:
-=== Surface meshes: ===
+ * Nifti-1 (.nii, .nii.gz)

'''Surface meshes'''

 * ASCII (.tri)
-Line 144:
+Line 327:
- * !BrainSuite (.dsgl, .dfs)
 * !FreeSurfer
 * FSL: VTK (*.vtk)
 * FSL: Geomview (*.off)
 * ASCII (.tri)
+ * BrainSuite (.dsgl, .dfs)
 * Curry BEM surfaces (.db*, .s0*)
 * FreeSurfer (lh.*, rh.*)
 * FSL: VTK (.vtk)
 * FSL: Geomview (.off)
 * MNI obj (.obj)
-Line 150:
+Line 334:
-=== Noise statistics (sensor covariance arrays): ===
 * Neuromag / MNE (.fif)
 * ASCII arrays

=== Dipole models: ===
 * Elekta Neuromag XFit (.bdip)
+ * SimNIBS/Gmsh (.msh)
 * 3D masks or atlases from MRI files

<<HTML(</TD></TR></TABLE>)>>

== Development, release and distribution ==
Brainstorm follows a '''continuous development and release model'''. Brainstorm is updated on a rolling basis to ensure that users have access to the latest features, improvements and bug fixes as soon as they are ready. These updates are regularly published on the [[https://github.com/brainstorm-tools/brainstorm3|Brainstorm GitHub repository]], and the version in the [[https://neuroimage.usc.edu/bst/download.php|download page]] are updated everyday.

Updates can be obtained:

 * '''Automatically''': at the Brainstorm startup, the user gets notified for updates and can download a new version is necessary.

 * '''Manually''': this is be started within the GUI with the menu '''Update > Update Brainstorm'''

 * '''GitHub''': for users and developers experienced in git and GitHub, latest Brainstorm source code can be retrieved from the Brainstorm GitHub repository.