Differences between revisions 65 and 92 (spanning 27 versions)

Introduction

Brainstorm is a collaborative open-source Matlab application dedicated to magnetoencephalography (MEG) and electroencephalography(EEG) data visualization, processing and cortical source estimation. Our intention is to make a comprehensive set of tools available to the scientific community involved in MEG/EEG experimental research.For physicians and researchers, the interest of this software package resides in its rich and intuitive graphic interface, which does not require any programming knowledge.

What you can do with Brainstorm

MEG / EEG recordings:
- Reading data from the most popular file formats (list here)
- Interactive access to the original files, or copy in the database
- Reviewing and editing of event markers in continuous files
Pre-processing:
- Epoching
- Detection of bad trials / bad channels
- Baseline correction
- Frequency filtering
- Resampling
- Averaging
- Noise covariance estimation
Recordings visualization:
- Various time series displays
- Data mapping on 2D or 3D surfaces
- Generate slides and animations
- Channel selection, and manipulation of clusters of electrodes
MRI visualization and coregistration:
- Analysis on individual anatomy or MNI / Colin27 brain
- Import MRI and meshes from most of the existing file formats (list here)
- Co-registration with the MEG/EEG coordinate system
- Volume rendering (several display modes)
- Deformation of the MNI template to fit an set of digitized head points
Database:
- Classification of recordings with three levels of definition (protocol, subject, condition/event)
- Quick access to all the data in a study
- Quick comparison between subjects or conditions
- Graphical batching tools (apply a same process to many files in a few clicks)
Forward modeling:
- MEG: Single sphere, overlapping spheres
- EEG: Berg's three-layer sphere
- Interactive interface to define the best fitting sphere
Inverse modeling:
- L2 Minimum-norm current estimates
- dSPM
- sLORETA
- All methods can be cortically constrained or not, and with constrained orientations or not
Source display and analysis:
- Surface and volume rendering of the estimated sources
- Re-projection of the sources in the MRI volume
- Definition of cortical regions of interest (scouts)
- Re-projection of estimated sources on a surface with a higher or lower definition
- Spatial smoothing before group analysis
- Easy screen captures, creation of movies and contact sheets
- Import and display of xfit dipoles
Time-frequency analysis:
- Time-frequency decomposition of recordings and sources time series using Morlet wavelets
- Time and frequency scales: linear or bands
- Many display modes available
Group analysis:
- Registration of individual brains on the MNI "Colin27" brain
- Statistical analysis (t-tests, permutations)
Documentation and support:
- Easy and automatic updates of the software
- Detailed step by step tutorials for most of the common features
- Active user forum

What you cannot do with Brainstorm

Intensive pre-processing of MEG/EEG recordings (noise cancelling, artifact correction/rejection, etc.):
=> use your constructor's software, or other software solutions (MNE, EEGLab, FieldTrip, etc.). ?See here.
MRI segmentation:
=> use FreeSurfer, BrainSuite or BrainVisa. ?See here.

Supported file formats

EEG:

EGI NetStation epoch-marked file (.raw/.epoc)
Neuroscan (.cnt, .eeg, .avg, .dat)
BrainAmp (.eeg)
EEGLab sets (.set)
Cartool simple binary files (.ep, .eph)
ErpCenter (.erp/.hdr)
Any type of ASCII arrays

MEG:

CTF (.ds directory)
Neuromag FIFF (.fif)
BTi / 4D Neuroimaging
LENA format

Sensors locations:

Cartool (.xyz, .els)
BESA (.sfp, .elp, .eps/.ela)
Polhemus Isotrak (.pos, .elp)
Curry (.res, .rs3)
EEGLab (.ced, .xyz, .set)
EETrak (.elc)
EGI (.sfp)
EMSE (.elp)
Neuroscan (.dat, .tri)
ASCII arrays

MRI volumes:

CTF (.mri)
GIS (.ima/.dim) -- (brainVISA: )
Analyze (.img/.hdr)
Nifti-1 (.nii)
Neuromag (.fif)
MGH (.mgh, .mgz)

Meshes:

BrainVISA (.mesh)
BrainSuite (.dsgl, .dfs)
FreeSurfer
ASCII (.tri)
Neuromag (.fif)

Noise covariance matrix:

Neuromag / MNE (.fif)
ASCII arrays

-  ⇤ ← Revision 65 as of 2009-09-11 21:43:31 → 
  Size: 2580
  Editor: hirkania
  Comment:
+   ← Revision 92 as of 2011-05-09 23:29:44 → ⇥
  Size: 4692
  Editor: cpe-76-169-10-66
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-!Brainstorm is an integrated free Matlab toolbox dedicated to Magnetoencephalography(MEG) and Electroencephalography(EEG) data visualization and processing. Our intention is to make a comprehensive set of tools available to the scientific community involved in MEG/EEG experimental research.
+||<tablewidth="100%">Brainstorm is a collaborative open-source Matlab application dedicated  to magnetoencephalography (MEG) and electroencephalography(EEG) data  visualization, processing and cortical source estimation. Our intention  is to make a comprehensive set of tools available to the scientific  community involved in MEG/EEG experimental research.For physicians and  researchers, the interest of this software package resides in its rich  and intuitive graphic interface, which does not require any programming  knowledge. || {{attachment:logo.gif||height="158px",width="262px"}} ||
 Line 4:
-== What you can do with BrainStorm ==
 * Import MEG / EEG recordings from the most popular file formats ([[FileFormats|list here]])
-Line 7:
+Line 5:
- * Data visualization:
+== What you can do with Brainstorm ==
 * MEG / EEG recordings:
  * Reading data from the most popular file formats ([[#line-78|list here]])
  * Interactive access to the original files, or copy in the database
  * Reviewing and editing of event markers in continuous files

 * Pre-processing:
  * Epoching
  * Detection of bad trials / bad channels
  * Baseline correction
  * Frequency filtering
  * Resampling
  * Averaging
  * Noise covariance estimation

 * Recordings visualization:
-Line 9:
+Line 24:
-  * Data mapping on the head surface
+  * Data mapping on 2D or 3D surfaces
-Line 11:
+Line 26:
-  * Channel selection
  * Data filtering
  * 3D surface rendering
+  * Channel selection, and manipulation of clusters of electrodes
-Line 16:
+Line 29:
-  * Import MRI scans, from most of the existing file formats ([[FileFormats|list here]])
+  * Analysis on individual anatomy or MNI / Colin27 brain
  * Import MRI and meshes from most of the existing file formats ([[#line-78|list here]])
-Line 18:
+Line 32:
-  * Volume rendering
+  * Volume rendering (several display modes)
  * Deformation of the MNI template to fit an set of digitized head points
-Line 24:
+Line 39:
-  * Graphic batching tools (apply a same process to many files in a few clicks)
+  * Graphical batching tools (apply a same process to many files in a few clicks)
-Line 27:
+Line 42:
-  * Single sphere method
  * Overlapping spheres method
  * Realistic head models using BEM and FEM
+  * MEG: Single sphere, overlapping spheres
  * EEG: Berg's three-layer sphere
  * Interactive interface to define the best fitting sphere
-Line 31:
+Line 47:
-  * Minimum-norm imaging of the cortical current density
+  * L2 Minimum-norm current estimates
  * dSPM
  * sLORETA
  * All methods can be cortically constrained or not, and with constrained orientations or not

 * Source display and analysis:
  * Surface and volume rendering of the estimated sources
  * Re-projection of the sources in the MRI volume
  * Definition of cortical regions of interest (scouts)
  * Re-projection of estimated sources on a surface with a higher or lower definition
  * Spatial smoothing before group analysis
  * Easy screen captures, creation of movies and contact sheets
  * Import and display of xfit dipoles
 * Time-frequency analysis:
  * Time-frequency decomposition of recordings and sources time series using Morlet wavelets
  * Time and frequency scales: linear or bands
  * Many display modes available
-Line 37:
+Line 69:
-== What you cannot do with BrainStorm ==
 * Intensive pre-processing of MEG/EEG recordings (noise, artifact correction/rejection, re-averaging, etc.):<<BR>> => use your constructor's software, or other software solutions (MNE, EEGLab, etc.). [[Links|See here]].
+ * Documentation and support:
  * Easy and automatic updates of the software
  * Detailed step by step tutorials for most of the common features
  * Active user forum

== What you cannot do with Brainstorm ==
 * Intensive pre-processing of MEG/EEG recordings (noise cancelling, artifact correction/rejection, etc.):<<BR>> => use your constructor's software, or other software solutions (MNE, EEGLab, !FieldTrip, etc.). [[Links|See here]].
-Line 42:
+Line 79:
-== Requirements ==
!BrainStorm is written in Matlab code only, thus it can run on any operating system supported by Matlab (including Windows, Linux, MacOS...).
+== Supported file formats ==
=== EEG: ===
 * EGI !NetStation epoch-marked file (.raw/.epoc)
 * Neuroscan (.cnt, .eeg, .avg, .dat)
 * !BrainAmp (.eeg)
 * EEGLab sets (.set)
 * Cartool simple binary files (.ep, .eph)
 * !ErpCenter (.erp/.hdr)
 * Any type of ASCII arrays
-Line 45:
+Line 89:
-If you have a Matlab licence:
+=== MEG: ===
 * CTF (.ds directory)
 * Neuromag FIFF (.fif)
 * BTi / 4D Neuroimaging
 * LENA format
-Line 47:
+Line 95:
- * You can download and run directly the !BrainStorm source scripts,
 * Minimum Matlab version: 7.1 (= R14-SP3)
 * Minimum Java VM version: 1.5 (To check that: type "ver" at Matlab command prompt)
+=== Sensors locations: ===
 * Cartool (.xyz, .els)
 * BESA (.sfp, .elp, .eps/.ela)
 * Polhemus Isotrak (.pos, .elp)
 * Curry (.res, .rs3)
 * EEGLab (.ced, .xyz, .set)
 * EETrak (.elc)
 * EGI (.sfp)
 * EMSE (.elp)
 * Neuroscan (.dat, .tri)
 * ASCII arrays
-Line 51:
+Line 107:
-If you do not have a Matlab licence:
+=== MRI volumes: ===
 * CTF (.mri)
 * GIS (.ima/.dim) -- (brainVISA: {{http://brainvisa.info}} )
 * Analyze (.img/.hdr)
 * Nifti-1 (.nii)
 * Neuromag (.fif)
 * MGH (.mgh, .mgz)
-Line 53:
+Line 115:
- * You can download the !BrainStorm binaries corresponding to your operating system.
 * The executables are build using the Matlab Compiler (mcc)
 * They will install automatically the Matlab Component Runtime (MCR) on your computer, a freely redistributable library
+=== Meshes: ===
 * BrainVISA (.mesh)
 * !BrainSuite (.dsgl, .dfs)
 * !FreeSurfer
 * ASCII (.tri)
 * Neuromag (.fif)

=== Noise covariance matrix: ===
 * Neuromag / MNE (.fif)
 * ASCII arrays

Software

Users

Development