Diff for "Introduction"

Differences between revisions 550 and 629 (spanning 79 versions)

News

Problems with automatic updates: Read this page

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)
sEEG/ECoG: Boundary Element Models (with OpenMEEG)
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

ANT ASA (.msm/.msr)
ANT EEProbe (.cnt, .avr)
BDF / BDF+ (Biosemi 24bit binary)
BESA exports (.avr, .mul)
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)
MEGA NeurOne (.bin)
Micromed (.trc)
Muse (.csv)
Neuralynx (.ncs)
Neurodata Without Borders (.nwb)
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

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 (.hdf5)
MEG-BIDS formatted databases

fNIRS

Brainsight NIRS (.nirs)
SNIRF (.snirf)

Other recordings

EyeLink eye tracker (.edf)

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

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- * '''New courses''': Beijing (April 8-9), Montreal (May 1-2), London (June), ... [[Training|Register]]
+ * <<HTML(<FONT color="#DD0000">)>>'''Problems with automatic updates'''<<HTML(</FONT>)>>: [[https://github.com/brainstorm-tools/brainstorm3/issues/308#issuecomment-646026943|Read this page]]<<HTML(<!--)>>
 * '''New courses''': Kentucky (Fall) -  [[Training|Register]]<<HTML(<!--)>>
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- * <<HTML(<FORM     METHOD="get" onSubmit='searchforum(this); return false'><B>Search the user forum</B>: <INPUT type='text' id='txtforum'  size=25 style="height: 22px; padding: 0px 10px 0px 10px;"></FORM>)>>
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-Brainstorm is a collaborative, open-source application dedicated to the analysis       of brain recordings: <<BR>>MEG, EEG, fNIRS, ECoG, depth electrodes and animal       electrophysiology.
+Brainstorm is a collaborative, open-source application dedicated to the analysis       of brain recordings: <<BR>>MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.
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-Since the project started by the end of the 1990's,  our server has registered more than 14,000 accounts. See our [[Pub|reference page]] for a list of published studies featuring Brainstorm at work.
+Since the project started by the end of the 1990's,  our server has registered more than 27,000 accounts. See our [[Pub|reference page]] for a list of published studies featuring Brainstorm at work.
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+<<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(<!-- )>>
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+<<HTML( -->)>>
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-This software was generated primarily with support from the National Institutes of Health under grants 2R01-EB009048, R01-EB009048, R01-EB002010 and R01-EB000473.
+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.
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-'''MEG/EEG recordings:'''
+'''MEG/EEG recordings'''
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+Line 62:
- * Support for multiple modalities: [[Tutorials/Auditory|MEG]], [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG]], [[http://neuroimage.usc.edu/brainstorm/News#February_2015|sEEG]], [[http://neuroimage.usc.edu/brainstorm/News#February_2015|ECoG]], [[http://neuroimage.usc.edu/brainstorm/News#June_2015|animal LFP]], [[Tutorials/NIRSFingerTapping|NIRS]]
+ * 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]]
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-'''Powerful and versatile visualization: '''
+'''Powerful and versatile visualization '''
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-'''MRI visualization and coregistration: '''

 * Generate surfaces from MRI volume:  head, inner skull and outer skull | [[Tutorials/TutBem|link]]
 * Use individual or template anatomy  (MNI / Colin27 or ICBM152 brain) | [[Tutorials/DefaultAnatomy|link]]
 * Template anatomy can be warped to individual head surface | [[Tutorials/TutWarping|link]]
 * Import MRI volumes and tessellated surface envelopes | [[Tutorials/ImportAnatomy|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]]
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-'''Graphical batching tools''':
+'''Graphical batching tools'''
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-'''Head modeling: '''
+'''Head modeling '''
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-'''Source modeling: '''
+'''Source modeling '''
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+ * 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]]
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-'''Source display and analysis: '''
+'''Source display and analysis '''
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-'''Time-frequency decompositions: '''
+'''Time-frequency decompositions '''
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-'''Functional connectivity''':

 * Correlation, coherence, Granger causality, phase-locking value
 * Phase-amplitude coupling estimation
+'''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]]
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-'''Group analysis: '''
+ * 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 '''
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- * Standard group analysis pipeline | [[Tutorials/VisualSingle|single subject]] | [[Tutorials/VisualGroup|group]]
+ * Standard group analysis pipeline | [[Tutorials/VisualSingle|single subject,]] [[Tutorials/VisualGroup|group]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/Workflows|roadmaps]]
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-'''Documentation and support: '''
+'''Documentation and support '''
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- * ANT EEProbe continuous (.cnt)
+ * ANT ASA (.msm/.msr)
 * ANT EEProbe (.cnt, .avr)
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+ * CED Spike2 (.smr, .smrx, .son)
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+ * Curry 6-7 (.dat/.dap/rs3)
 * Curry 8 (.cdt/.dpa)
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+ * ERPLab results (.erp)
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+ * EGI-Philips (.mff)
 * EmotivPRO (.edf)
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- * g.tec / g.Recorder Matlab exports (.mat)
+ * g.tec / g.Recorder (.mat, .hdf5)
 * Intan (.rhd, .rhs)
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+ * Micromed (.trc)
 * Muse (.csv)
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+ * Neurodata Without Borders (.nwb)
 * NeurOne (.bin)
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- * NeuroScope (*.eeg;*.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)
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+'''Surface atlases'''

 * BrainSuite (.dfs)
 * FreeSurfer (.annot, .label)
 * Gifti texture (.gii)
 * SUMA atlas (.dset)
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- * Yokogawa / KIT
+ * Ricoh MEG (.sqd, .con, .raw, .ave)
 * Yokogawa / KIT (.sqd, .con, .raw, .ave)
 * York Instruments MEGSCAN (.hdf5)
 * MEG-BIDS formatted databases

'''fNIRS'''

 * Brainsight NIRS (.nirs)
 * SNIRF (.snirf)
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- * Brainsight NIRS (.nirs)
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+ * Localite (.csv)
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+ * SimNIBS (.csv)
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+ * DICOM (using SPM converter)
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-'''Surface atlases'''

 * BrainSuite (.dfs)
 * FreeSurfer (.annot, .label)
 * Gifti texture (.gii)
 * SUMA atlas (.dset)

<<HTML(</TD><TD>)>>
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+ * ASCII (.tri)
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- * ASCII (.tri)
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+ * SimNIBS/Gmsh (.msh)

Software

Users

Development

News

Support

How to cite Brainstorm

What you can do with Brainstorm

Supported file formats