Differences between revisions 431 and 444 (spanning 13 versions)

What's new

Brainstorm is in a very active development state: small or major bug fixes and improvements are issued almost everyday. To update your version of the software easily: Install and update.
See also the full list of updates: brainstorm3/doc/updates.txt | All github commits

July 2018

Updated dSPM 2018

Major modification in "Compute sources [2018]":
dSPM values are no longer scaled by number of trials. See source tutorial.

Interface

Headless mode: Brainstorm now runs without any rendering capability, allowing the execution of scripts on distant servers and computation clusters that do not have any display attached to them. Adding snapshots to the execution reports is still possible. Start your script with "brainstorm server".
Custom montage shortcuts: In the montage editor, shortcuts can now be associated with any montage in the list.
Stat duration threshold: Added "Minimum duration" threshold in the stat tab.
New montage: "Average reference (L -> R)" for 10-20 EEG caps

Anatomy

BrainSuite: Now reading subcortical structures from the SVReg atlas. See details.
OpenMEEG: Switched to version 2.4, which should increase stability and reliablity.

April 2018

Input/output

Support for g.tec HDF5 files
Support for Curry 6-7-8 EEG recordings
Support for Muse .csv EEG recordings
Montage can be loaded and saved as CSV files

ICA cleaning

Added option: Sort components based on correlation with a channel (EOG, ECG...)
Changed reconstruction method: (Winv_good * W_good) => (eye() - Winv_bad * W_bad)

March 2018

SEEG/ECOG

Updated tools for ECOG (new display options, many bug fixes)
New 2DLayout display option
Allow simultaneous display of SEEG and ECOG
Local average reference: Now available for all the groups of contacts

Bug fixes

All "Filter" processes were replacing the actual data with the "Std" field
Added legends to connectivity matrices displayed as images
Added support for Matlab 2018a

February 2018

Anatomy

FreeSurfer: Import the vox2ras matrix from the .mgz MRI files (ignored until now)
FreeSurfer: Correct registration of additional .nii files with full FreeSurfer anatomy folders
Export NIfTI: Exporting vox2ras transformation to .nii when volume was not initially .nii
MRI 3D: New options "Upsample image" to smooth MRI display in 3D figures
New option to add the ASEG atlas and the white matter surface to any 3D figure

Source modeling 2018

New version of the linear inverse models: bug fixes and support for mixed head models
Previous models will remain available as "Compute sources 2016"
Documentation: Source estimation tutorial

January 2018

Input/output

Support for the new RICOH MEG file format
Improved BIDS-MEG importer: derivatives folder (FreeSurfer, MaxFilter), acquisition info (_scans.tsv)
Fixed EEGLAB reader: Keep events in epochs, allow epochs with multiple event occurrences
Keep acquisition dates in the database (DateOfStudy of the brainstormstudy.at files)

Processes

Noise covariance: Match automatically noise covariance with subjects by acquisition date
Average: Added option "median"

November 2017

New tutorial: SEEG epileptogenicity maps

The tutorial SEEG epileptogenicity maps illustrates all the new features related with SEEG/ECOG: coregistration of MRI and CT scans, placement of depth electrodes in the post-implantation scans, SEEG bipolar montages, display and processing of intracranial recordings, computation of epileptogenicity maps.

Bug fixes

Matlab 2017b: A bug in isosurface.m caused irregularities in head surfaces
More guided protocol creation to avoid user errors and massive deletions of external folders

October 2017

Anatomy

New options for volume coregistration of multiple scans of the same subject (MRI/MRI or MRI/CT)
New interface for placing SEEG/ECOG contacts in the MRI Viewer
MRI viewer: Various interface improvements (zoom, shortcuts)
MRI viewer and MRI-3D: New menu Jump to maximum (shortcut "M")

SEEG/ECOG

Various improvements for handling SEEG/ECOG data: Import menus, montages, display
Add event markers on the signals when the event names match the channel names
New tab Guidelines for computing epileptogenicity maps

September 2017

Elekta: Major workflow changes

When importing Elekta .fif files, the default acquisition SSP are not applied by default anymore. These SSP projectors were previously always used in Brainstorm for visualization and source estimation. However, they were meant to be used only to review online recordings from the acquisition computer.
Now they are still imported but inactive by default. If you want to use them, for instance for backward compatibility purposes, enable them in the window "Select active projectors". If your recordings now look particularly ugly, our advice is to recompute SSP projectors with Brainstorm, rather than using the default acquisition ones.

Input/output

New DICOM converter (SPM-based): Use menu "Import MRI" and select file format "MRI: DICOM"
Export figures to Plotly: See tutorial
Export volume grids as .nii
Import channel files in .tsv format (IntrAnat)

August 2017

New processes

Epilepsy > Epileptogenicity maps: See tutorial
Frequency > Time-resolved phase amplitude coupling (tPAC): See tutorial
Frequency > FieldTrip: ft_mtmconvol (Multitaper)
Connectivity > Phase transfer entropy
Artifacts > Undo 4D/CTF noise compensation

July 2017

Anatomy

SEEG/ECOG: New option to import sensor positions in subject or MNI coordinates
Computation of SPM canonical surfaces (alternative to FreeSurfer/BrainSuite/BrainVISA)
New anatomy template: USCBrain
MRI registration: New option to reslice based on the NIfTI sform/qform transformations
Surfaces: Load .gii files as surface textures

Recordings viewer

New buttons for zooming vertically
New buttons for displaying the vertical and horizontal grids
Resize the display page with the red square at the bottom of the figure
File viewer made stand alone with the new function bst_autopilot.m
Optimized reviewing speed: New option "Downsample recordings for faster display"

Support for high-resolution screens

If you have a high-resolution screen, the text and icons in the Brainstorm window may not scale properly, leading the interface to be impossible to use. Select the menu File > Edit preferences, the slider at the bottom of the option window lets you increase the ratio of the Brainstorm interface.

May 2017

New file formats

EEG: Support for Nicolet .e files
EEG: Support for ANT ASA .msm/.msr files
EEG: Ugraded ANT EEProbe library for supporting recent files
EEG: Support for ERPLab files
Electrophysiology: Support for CED Spike2 .smr
Electrophysiology: Support for Ripple Trellis NEV/NSx files
Electrophysiology: Support for Backrock .ns6 files
Export to EDF: Now Brainstorm can be used to convert any file format to EDF

Major bug fixes

SSP: When epoching recordings (importing blocks of recordings to the database) from continuous files that were filtered AFTER doing the SSP/ICA cleaning, the SSP/ICA projectors were not properly reported in the channel file of the new imported folder. This was leading later on to a lack of accuracy in the estimation of the sources.
EEG: Neuroscan .cnt files with low accuracy (int16) were not read correctly

April 2017

New display for ECoG and sEEG

Many new options are available to render sEEG/ECoG recordings or power: interpolations on the cortex surface, in the MRI volume, or 2D displays of the time series.

Default fiducials from MNI template

When using the digitized head shape for aligning the MEG/EEG sensors on the MRI, the fiducial points NAS/LPA/RPA do not need to be placed very precisely as they are used only as a first approximation. Computing the MNI transformation for the MRI now sets default positions for the NAS/LPA/RPA fiducial points, you can use these if the accurracy of their location is sufficient. This option allows a fully automatic import of the anatomy+recordings.

March 2017

New file formats

EEG: Support for Micromed EEG TRC files
EEG: Support for Nihon Kohden .EEG files (including newer 1200 systems)
EEG: Export/import continuous recordings with SPM (.mat/.dat)
SEEG/ECOG: Import contact positions in MNI coordinates
Events: Support for Presentation .log files

Other improvements

New process: Connectivity > Amplitude envelope correlation
Anatomy: Apply manual sensor-MRI registration to multiple datasets
GUI: Added option to filter files by the comment of their parents

January 2017

New tutorial: Human Connectome Project (MEG)

The tutorial Human Connectome Project: Resting-state MEG explains how to download MEG recordings from the Human Connectome Project (HCP) ConnectomeDB database and process them into Brainstorm.

November 2016

New tutorial: OMEGA database & resting state (MEG)

The Open MEG Archive (OMEGA) offers for download a large database of resting state MEG recordings. The tutorial MEG resting state & OMEGA database describes how to access this database, download a few subjects and process them in Brainstorm.

BIDS specification

The Brain Imaging Data Structure (BIDS) standard for neuroimaging data organization was first established for MRI and fMRI (Gorgolewski, 2016). It is based on simple file formats and folder structures that can readily expand to additional data modalities.

An extension of the BIDS for MEG datasets is currently under review. One objective is that analysis pipelines designed with major analysis tools (such as Brainstorm, FieldTrip, MNE, SPM and others) can be readily applied without requiring software or pipeline redevelopments.

We have implemented functions that load automatically into a Brainstorm database any dataset following the BIDS specification. This prototype is illustrated in the tutorial MEG resting state & OMEGA database.

Volume atlases

Volume atlases in subject space (eg. FreeSurfer's Aseg atlas) can be used in various ways:

Import as scouts for volume source models: See Volume source estimation.
Import as volume: Import the aseg.mgz file as a new MRI in the subject anatomy folder, then display it with the MRI viewer. New colormaps are available for representing labelled atlases.

Volumes in MNI space

Volumes in MNI space can be imported and transformed to the subject space. This allows the new features described above also for standard volume atlases, such as the AAL atlas. You just need to make sure you select the file format "Volume mask or atlas (MNI space)" in the import options.

Import MNI volume atlases as scouts for volume source models.
Import MNI volume atlases as a subject volume, for overlaying on the subject structural MRI.
Import MNI volume atlases as surfaces (produces something similar to the "aseg" surface file).
To get the labels of the atlas displayed correctly, a .txt file with the same name should be present in the folder. Each line in this file must include the index of the label ("label_index label_name"), such as the atlases distributed as part of the MRIcron software.

CT-MRI coregistration

The volume registration functions allow to import a CT scan in the anatomy folder of the subject, and then to overlay it with the MRI to mark sEEG or ECoG contacts. This solution computes a linear MNI transformation for both volumes (CT and MR) and applies the two transformations to the new imported CT.

Extended source space

Head grid: The source space can be extended to the full head volume, this can help decide whether some sources are brain signals or artifacts (eg. eye movements or neck muscles, as illustrated below).

Import FreeSurfer anatomy: Creates an additional surface with the cerebellum by default.

FieldTrip: Improved support

Many new FieldTrip functions are now supported, especially for forward and inverse modeling:

ft_volumesegment: MRI volume segmentation (scalp, skull, brain)
ft_prepare_leadfield: Computation of forward models (calling also ft_prepare_headmodel)
ft_sourceanalysis: Inverse models (beamformers and minimum norm)

Previously made available:

ft_dipolefitting: Dipole fitting for MEG and EEG recordings
ft_channelrepair: Replacement of bad sensor with an average of the neighbors
ft_scalpcurrentdensity: Estimate of the SCD fields
ft_timelockstatistics: Statistics at the sensor level
ft_sourcestatistics: Statistics at the source level
ft_freqstatistics: Statistics in time-frequency space

Most data types can be converted easily between Brainstorm and FieldTrip structures (MRI, surfaces, sensors, recordings, head models, source maps, time-frequency results):

Right-click on any file > File > Export to file > Look for the FieldTrip option in the file formats.
toolbox/io/out_fieldtrip_*.m: Functions to convert from Brainstorm to FieldTrip structures.
toolbox/io/in_*_fieldtrip.m: Functions to load FieldTrip structures as Brainstorm structures.

October 2016

Brainstorm on GitHub

Star

We moved all the code of Brainstorm to a public GitHub repository. You're welcome to join!

https://github.com/brainstorm-tools/brainstorm3

New band-pass filters

The frequency filters have been notably improved. They have been completely redesigned and are now fully documented in the tutorial Frequency filters. From the process "Pre-process > Band-pass filter", you can display the filter response in frequency and time domain, together with all its properties.

After filtering signals, new events indicate the transient durations to consider. This represents an absolute minimum, if possible always exclude the full filter length, documented in the filter response window.

This modification has some impact in many processes using the band-pass filters: the SSP computation, the Hilbert transform, the visualization. These new filters are slightly slower but much more accurate. If reproducibility is a concern, use can select "Use old implementation" in the process options.

Other improvements

New process: Events > Detect cHPI activity (Elekta)
Volume scouts: Improved rendering and constrained growth now enabled
Volume scouts: Can be exported as volume masks (menu Scouts > Export as MRI mask)
Snapshots: Frequency contact sheets
Forum: Added full text search on the forum using Google (available on the home page of the website)
GUI: Support for high-DPI screens (Retina and other 4K displays)
GUI: Support for Matlab 2016b

August 2016

2D topography plots

The projection of the EEG/MEG recordings on 2D maps have been updated. The new functions are more stable and the figures will be easier to integrate directly in your publications.

Mixed head models

The basic source reconstruction limits the source space to the left and right hemispheres of the brain. The mixed head models allow to include the cerebellum and various subcortical regions to the estimation and the visualization of the source activity. Their support has been extended to include new features:

Projection on an anatomy template for group analysis.
The regions without orientation constrains are now flattened before the projection on the template (the source orientation is not a meaningful parameter at the group level).
Additionally, the sources on the template anatomy can now be re-projected in the subject space.
New exploded view to visualize all the subcortical regions on the same view.

MRI coregistration

You may be interested in importing multiple volumes (MRI, fMRI, CT, PET, etc) in the anatomy folder of a subject. You can overlay volumes and compare the results obtained with different imaging modalities or at various stages of a surgical procedure, or use fMRI results in an ROI analysis of you MEG/EEG recordings. However these various volumes usually have different orientations or spatial resolutions, and in order to be displayed in the MRI Viewer in Brainstorm, the files must have the same size and same orientation. We added some functions to help you coregister these volumes.

New menu "Resample MRI" to reslice any MRI volume.
New menu "Register on default MRI" to co-register multiple MRI volumes of the same subject.
These two options are offered when importing additional volumes in the subject anatomy, if their dimensions or resolution do not match the initial structural MRI.
The computation of the MNI transformation is now available for all the MRI volumes (before this was restricted to isotropic volumes with a voxel size of 1x1x1mm). This option first resamples the volume to a 256x256x256 volume with a unit voxel size, and then runs the SPM8-based affine MNI registration.
When you have a secondary volume imported in your subject, you can display it as an overlay on the original MRI and configure the threshold and transparency from the Surface tab.

Updated advanced tutorials

Many of the advanced tutorials were outdated, they have all been updated to include the latest advances in cleaning procedures, workflow management and display.

EEG/Epilepsy: Includes a new section about ICA decomposition.
Elekta-Neuromag median nerve: Reference for processing Elekta MEG recordings.
Yokogawa/KIT median nerve: Reference for processing Yokogawa/KIT/Ricoh MEG recordings.
CTF median nerve tutorial: Dataset used in the previous version of the introduction tutorials.

Other advanced tutorials that have been improved recently:

July 2016

New tutorial: Group analysis

This new tutorial reproduces in the Brainstorm environment the analysis described in the SPM tutorial "Multimodal, Multisubject data fusion". The data processed here consists of simultaneous MEG/EEG recordings from 19 participants performing a simple visual recognition task from presentations of famous, unfamiliar and scrambled faces. The analysis is split in two tutorial pages: the analysis of a single subject and the group analysis.

This is part of a new effort in cross-validating the various academic programs for EEG/MEG analysis (EEGLAB, FieldTrip, SPM, MNE). The results will be presented at a satellite meeting at the Biomag conference, held in Seoul on October 2nd.

New tutorial: Scripting

Advanced users who want to go beyond the limits of the graphic interface, script large studies or add their own routines to the software now have access to an introduction to the Brainstorm API. The tutorial Scripting explains how to interact with the software from the Matlab command line or a .m script.

Volume sources

The support for volume source models has been improved and now includes new features:

Implementation of volume scouts: Volume source estimation tutorial.
Projection on an anatomy template for group analysis: Subjects coregistration tutorial.

Anatomy: Defining the fiducials

We propose a new pipeline for processing and importing the anatomy for multiple subjects. This is described in this section of the Scripting tutorial: How to process an entire study.

New menu "File > Batch MRI fiducials": Sets the anatomical landmarks for all the subjects.
MRI Viewer: New popup menu "Save fiducial file".

June 2016

Continuous recordings

New popup menu "File > Copy to database": Copies a native continuous file to the protocol folder, in order to make the database portable between computers.
New menu "File > Export protocol > Copy raw files to database": Does the same as "Copy to database" for all the continuous files available in the current protocol.
Continuous files can now be resampled with the process "Pre-process > Resample".
New menu "File > Load protocol > Change database folder": Changes the folder in which the new protocols are created, but does not have any impact on the existing protocols.
Process reports: Export the reports to HTML files (including the screen captures).

Statistics

Redesign of all the functions related with statistic testing. See the new Statistics tutorial.
New process(2): Test > Parametric test: Paired/Independent
New process(2): Test > Permutation test: Paired/Independent
New process(1): Test > Parametric test against zero
New process(1): Test > Parametric test against baseline
New process: Extract > Find maximum in time
New process: Extract > Find maximum in frequency
Allowed the execution of the averaging and statistics processes on the connectivity measures.

Default EEG caps

Added support for BioSemi caps with electrodes named "A1" instead of "A01".
Added support for EGI Hydrocel caps with electrodes named "E001" instead of "E1".
Organized the default electrode positions by manufacturer.

May 2016

New tutorial: fNIRS

Many new tools are available for importing manipulating fNIRS recordings in Brainstorm. This is explained in a new online tutorial (work in progress): NIRS finger tapping.

New tutorial: Elekta phantom

A new tutorial explains how to import and process Elekta-Neuromag current phantom recordings. The framework presented on this page is designed to be used for the quality control of an Elekta MEG system (after a maintenance for instance) and for evaluating dipole modeling techniques.
MEG current phantom (Elekta)

Baseline normalization

New process "Standardize > Baseline normalization" that replaces two existing processes: "Z-score normalization" and "Event-related perturbation (ERS/ERD)"
New recommendations for the normalization of source maps (never use an absolute value):
Source estimation tutorial (normalization).
Normalized source maps are now displayed with the same colormap as the original source maps.

Recordings viewer

Min/max: You can now quickly get the minimum and maximum values in the recordings by simply selecting a time segment. If some channels are selected, it shows the extrema only for them.
Overlay: The montage editor now supports a syntax for overlaying multiple signals. You just need to set multiple channels with the same display name.
Color: The montage editor now allows the direct definition of a color for specific channels: Use the specific syntax for the display name: "NAME|RRGGBB" (hexadecimal notation).
Make a database portable: New menu "Export protocol > Copy raw files to database".
Make a database portable: New popup menu for raw files "File > Copy to database".

Time-frequency

Hilbert transform: The new option "power" is now the default (instead of "magnitude" previously)
Now keeping track of the edge effects when extracting time windows from a larger file.
PSD: Estimation directly from source files attached to a raw link.
PLV: Added an option to save the magnitude.

April 2016

Major bug fix: BrainAmp

The gain of the channels in some BrainVision files (BrainAmp or V-Amp) was not read correctly.
The files impacted are the ones for which the gains are specified in the .vhdr/.ahdr files, in section [Channel Infos], field <Resolution in microvolts>.
To fix the problem: Delete all the imported files and links to continuous files and start over.

Scouts: Sign flip

Major modification in the computation of the scouts time series (constrained orientations only). Previously, the sign flip of sources with opposite directions was applied only if it increased the average scout amplitude. Therefore the procedure was dependent on the data, making it difficult to compare across conditions and subjects. Now the sign flip is always applied.
To disable completely the sign flip: Use the process "Extract > Extract scouts time series".

Source modeling

Major update of the new inverse interface (Compute sources [2016]).
Bug fix: Dipole scanning orientations were wrong for the unconstrained source maps.
Save whitened recordings: New menu available when right-clicking on source files in the database explorer. It shows how the recordings are actually used in the minimum norm source estimation, after the pre-whitening computed based on the noise-covariance matrix. If this doesn't look correct, you might think about changing the options for the noise covariance regularization (increasing or decreasing the amount of regularization.
Data covariance computation can now use a separate baseline window for DC removal.

Dipoles

New dipoles exploration panel (more details to come)

March 2016

Input / output

Support for FieldTrip raw data file (trials)
Convert imported files to continuous files: Right-click > Review as raw
Copy external raw files to the database: Right-click > File > Copy to database
Make the entire protocol portable: File > Export protocol > Copy raw files to database

Distribution

Script distribution: Added support for Matlab 2016a
Compiled distribution: Switched to Matlab 2015b (smaller and faster)
Compiled distribution: Does not crash anymore when Brainstorm is closed

February 2016

Major bug fix: MEG reference sensors

Bug fix: The geometry of the CTF MEG reference sensors was not imported correctly. The forward model was not as accurate as expected, especially with a very high signal-to-noise ratio.
For more accurate results, re-import the recordings and compute a new forward model.
Bug identified: Similarly, the 4D MEG reference gradiometers may not be modeled properly
(waiting for tests from any site with a 4D system)
New tutorial to investigate this problem: CTF current phantom
Channel file: New menu "Display sensors > CTF coils (ALL)" to represent the CTF reference sensors.
Similar menus available for 4D and Elekta-Neuromag systems.

Anatomy

New template BCI-DNI_BrainSuite: Description of the atlas | Brainstorm documentation
Replaced the default template Colin27 with ICBM152: Brainstorm documentation
Process "Sources > Spatial smoothing": Replaced with a function from the SurfStat toolbox

Parametric statistics

New functions for parametric tests (one-sample, two-sample, paired)
Histograms: Added the result of the Shapiro-Wilk test and a "Q-Q plot" button
New Process2: File > Select uniform number of files: Selects the same number of files in A and B

January 2016

Display as image

[Trials x Time] Right-click on a group of trials > Display as image: Raster plot for the values of one sensor across the trials. Change the channel from the Display tab (or up/down arrow key).
[Channels x Time] Right-click on one single file > MEG/EEG > Display as image:
Shows the same information as the "time series" view, but with colors instead of lines.

Synchronization with an eye tracker

A new tutorial from Martin Völker explains how to import the eye movements detected by an eye tracking device into an EEG/MEG file. The new generic process "Synchronize > Transfer events" can be used for synchronizing the event markers between files with different sampling rates.
See tutorial: Synchronization with eye tracker.

November 2015

Documentation

New introduction tutorials: Difference and Statistics
New button [Online tutorial] in the pipeline editor, to jump instantly to the corresponding tutorial.

Input / output

Support for EyeLink eye tracker recordings (.edf)
Support for g.tec Matlab exports (.mat)
Support for Brainsight NIRS systems (Homer file format)
Support for Cartool .mrk events file
Support for BESA .evt events file

Microstate segmentation

A new external plugin for microstate segmentation developed at John Cacioppo's lab (UChicago) has been made available publicly in Brainstorm. See the CENA website and the corresponding online tutorial.

October 2015

New processes

Standardize > Scalp current density (FieldTrip: ft_scalpcurrentdensity)
Standardize > Concatenate signals
Extract > Extract values: Generic process for extracting and concatenating blocks of files
File > Select uniform number of trials

Histograms

Display of value histograms for all the files in the database (right-click > File > View histogram)

September 2015

New introduction tutorials

We completely re-organized the tutorials page. A new set of introduction tutorials is now available for beginners to learn the basics and for expert users to find references and technical details. We added a lot of material to describe the improvements we brought to the software in the past five years.

We encourage advanced user to have a look at them to learn about the new features and the new best practice guidelines we came up with over the years.

Input / output

Support for ITAB MEG file format
Support for Neuralynx file format (.ncs)
Support for MEGA NeurOne file format (.bin)
Support for Blackrock NeuroPort file format (.nsX, .nev)
Support for BrainVision channel files (.bvct, .bvef)
Import FieldTrip structures: data_timelocked saved as .mat files
Export FieldTrip structures: source files, time-frequency maps and head models

Source modeling

Forward model: Generation of regular isotropic source grids
New process: Source > Dipole fitting (FieldTrip: process_ft_dipolefitting)

Anatomical registration with BrainSuite

BrainSuite now provides an accurate registration method to the BrainStorm anatomy templates (ICBM152, Colin27). See the BrainSuite tutorial.

August 2015

FieldTrip statistics

Some FieldTrip functions can be called from the pipeline editor in Brainstorm, this brings a lot of long-awaited tools for statistical analysis. See the Statistics tutorial.

Permutation-based non-parametric t-tests
Cluster-based correction for multiple comparisons
This is done with direct calls to FieldTrip functions:
ft_timelockstatistics, ft_sourcestatistics, ft_freqstatistics
New displays for exploring significant clusters

New anatomy template: One year old infant

Christian O'Reilly proposes a new anatomical atlas for one year old babies, described in this forum post: http://neuroimage.usc.edu/forums/showthread.php?2123-Atlas-for-1-year-old-babies

To use this template: create a new subject using an individual anatomy, right-click on the subject >
Use template > Download: Oreilly_1y.

Project scouts between subjects

A simple yet very powerful tool is now available to project a region of interest between surfaces: from different surfaces of a subject, or between a subject and a template. When using surfaces generated with FreeSurfer, this projection uses the accurate registration described in the coregistration tutorial.
In the Scout tab, this is available in the menu Scout > Project to...

Scouts from MNI coordinates

You can now start a scout from anatomical positions specified in MNI coordinates.
In the Scout tab, this is available in the menu Scout > New: coordinates.

Z-score normalization

Modifications were made to the Z-score process, specially for handling the normalization of sources:

The static and dynamic versions of the process were merged. Now the dynamic version is only called for the normalization of kernel-based source files.
Unconstrained sources: Now it first converts the unconstrained sources to flat maps by taking the norm of the three dipole orientations, then computes the Z-score of the norm.
The dynamic version does not save new shared kernels anymore, because it doesn not make much sense to compute the Z-score of single trials.

July 2015

New inverse functions

New functions are now available for solving the MEG/EEG inverse problems. Not all the options are publicly available yet, but they will be soon. See the new tutorial: Source estimation.

Artifact detection

A new process is available for helping with the detection of non-standard artifacts in MEG/EEG recordings: Events > Detect other artifacts. It is documented in the new tutorial Additional bad segments.

Decoding and MVPA

The recent work from Oliva's lab at MIT on decoding experimental conditions with MEG is now available as a process in Brainstorm. It allows to run support vector machine (SVM) and linear discriminant analysis (LDA) classification on MEG data across time. It is documented in the tutorial Decoding conditions.

Cichy RM, Pantazis D, Oliva A (2014)
Resolving human object recognition in space and time, Nature Neuroscience, 17:455–462.

Custom colormaps

Custom colormaps can be saved in the user preferences, edited and re-used easily. This is documented in the new colormap tutorial.

June 2015

Standard deviation/error

Two new options are available in the proces "Average files", to compute the standard deviant or the standard error together with the average. This additional information is stored in the field Std of the average files, and is displayed as a bounded line around the signals when available.

Synchronized videos

You can attach synchronized videos to the continuous file viewer. Right-click on the "link to raw file"
> File > Add synchronized video. There are many ways to sync EEG and videos, the mechanisms you use are probably not supported yet. Please contact us if you are interested in using this feature.

April 2015

Major bug fix: dSPM

The dSPM values displayed were not scaled properly in the following configuration: Shared dSPM kernel calculated for a folder that contains at the same time single trials and averages of these trials. Values were wrong when displaying the sources for the averaged files using this shared kernel.

The new values are multiplied on the fly by a fixed factor: sqrt(nAvg)
where nAvg is the number epochs that are were averaged to compute the average.

This issue is documented in the source estimation tutorial.

MNI coordinates

It is now possible to use MNI coordinates to navigate in the original individual MRI volumes. We estimate the affine transformation from the subject space to the MNI ICBM152 template using the SPM12 software (spm_maff8 ©J Ashburner). The general approach is described in the following article:
Ashburner J, Friston KJ, Unified segmentation, NeuroImage 2005

To compute the linear transformation matrix between the individual MRI and the ICBM152 template, click on Compute MNI transformation in the MRI Viewer or the popup menu for the MRI.

New functions are also available for converting between coordinate systems: cs_convert and cs_compute.

New processes

FieldTrip > ft_channelrepair
Standardize > Interpolate bad electrodes
Standardize > Normalized difference (A-B)/(A+B)
Standardize > ERDS with two inputs
Events > Detect multiple responses
Events > Detect movement
Test > Student's t-test against zero

Input / output

Export data files to FieldTrip structures (out_fieldtrip_data)
Export MRI overlay to MRI files (allows to export dipoles density)
New popup menu "Import data matrix" when right-clicking on a study folder

March 2015

EEG: Artifact cleaning with ICA

Many EEG users are familiar with the Independent Component Analysis (ICA) for identifying and correcting artifacts such as eye movements, muscle activity or 60Hz. We added methods implemented initially in EEGLAB for calculating ICA decompositions of MEG and EEG signals. The methods available for now are Infomax and JADE. We will add soon other methods widely used in the EEG community: SOBI and AMICA.

The ICA decomposition is available for continuous files only and can be found next to the SSP menus, either in the pipeline editor or in the Artifacts menu of the Record tab.

The SSP interface has been extended to select interactively the ICA components and display their spatial topography and time series.

EEG: Montage editor

Improved flexibility of the montage editor, for supporting some common operations in EEG analysis:

Support for linked EEG references.
Mixing channels from different modalities in the same montage. This is useful for re-referencing the EEG with an electrode that is not classified as "EEG" in the channel file. It allows also to review multiple types of signals in the same figure: EEG, EOG, ECG, EMG, etc.

EEG: Permanent re-referencing

EEG recordings can be re-referenced using projectors, similar to the ICA or SSP projectors. This allows to change permanently the reference without having to create a montage and explicitly apply it to the recordings. This feature is available in two ways:

Process: Standardize > Re-reference EEG
Record tab: menu Artifacts > Re-reference EEG

February 2015

Intra-cranial recordings

New options are available to display and process invasive recordings, sEEG (depth electrodes) and ECoG (grids of strips of subdural electrodes), developed in collaboration with the Cleveland Clinic and the Freiburg University Hospital.

New display mode: 3D Electrodes
Edit the position of the contact positions using the MRI Viewer.
Grouping contacts using the new field "Group" in the channel file. Use the channel file editor to modify these groups if they haven't been identified correctly (right-click > Edit channel file).
Set of temporary bipolar montages automatically created when loading SEEG/ECOG recordings.
Computation of the forward model for ECOG and SEEG concacts using the OpenMEEG BEM model.
These tools are still in development, we will document them with a tutorial when they are stable.

January 2015

Major bug fixes

Error in reading the BDF/EDF channel gains, the signal amplitudes were not scaled correctly
Error in the calculation of the scouts values with process_extract_scouts in the case of constrained sources and atlases with non-sorted vertices (older atlases loaded with new code)

New supported file formats

MEG: KRISS MEG .kdf file format
MEG: BabyMEG system
MEG: Neuromag Graph event .evl file format
EEG: Compumedics ProFusion Sleep 4 file format
Import EEGLAB: Added support for categories "latency" and "type"

New processes

Connectivity > Time-resolved correlation and coherence
Events > Convert to simple event
Events > Convert to extended event

December 2014

New processes

Standardize > Spectrum normalization: Corrects for 1/f decrease in power in TF and PSD results.
Pre-process > ARIMA filter: Spectral flattening of a signal (use before TF decomposition).
Average and statistics: All the processes grouping multiple subjects now save their results in a subject "Group analysis" instead of the "Inter-subject" node.

November 2014

Changes in scout processing

We made some important modifications to the way the scouts where handled in the processes. Now it is possible to select the atlas directly in the options of the process, and to process at the same time scouts from different subjects with different list of vertices.

The new process function for extracting scouts is process_extract_scouts (before it was process_extract_cluster). The scout option value in the process is now a cell array, instead of the full scout structure. Example: {'User scouts', {'Scout1', 'Scout2'}}

This will affect all the processes that use scouts: time-frequency decompositions, power spectrum estimates, connectivity and PAC metrics. We tried to keep all the processes compatible with the previous input format, but there might be some modifications to do in personal scripts. If you have processes that use scouts structures in input, you might need to edit them to accept this new format. You can look at how it is done in process_canoltymap.m, or contact us through the user forum for help with updating your scripts.

October 2014

New anatomy template: Infant 7 weeks

The anatomical atlas presented in Kabdebon's article Anatomical correlations of the international 10–20 sensor placement system in infants is made available as a template in Brainstorm. To use this anatomy: create a new subject using an individual anatomy, right-click on the subject > Use template > Download: Infant7w.

EEG electrodes positions

It is now easier to manage the 3D positions of the EEG electrodes. To add electrodes positions to an existing channel file: right-click on the channel file > Add EEG positions. You can import the points from a file or from one of the default sets of positions available in Brainstorm.

Brain Entropy in space and time

A tutorial is available online to introduce a new Brainstorm plug-in BEst: Brain Entropy in space and time which offers three new source localization approaches for EEG and MEG data, based on the framework of the Maximum Entropy on the Mean (MEM). These methods are particularly dedicated to estimate accurately the spatial extent of EEG/MEG generators with time series stable within parcels, to localize the generators of oscillatory patterns and synchrony.

Data export

All the files in the Brainstorm database can now be exported as ASCII, CSV and Excel files: channel positions, recordings, sources, time-frequency maps and connectivity matrices.

September 2014

Filtering continuous files

Major modifications were made to the way the continuous files are handled:

The continuous files saved by Brainstorm when applying a filter to a native file are now saved in a new file format (Brainstorm binary, extension .bst), regardless of the original file format. The values in this file are saved in floating point double precision to avoid the re-conversion to integer 16bit needed to save CTF of FIF files, which cause significant loss of data quality.
These files are not saved anymore in the same folder as the original data, but in the Brainstorm database itself. Removing the links to the processed files from the Brainstorm database now deletes the actual files.
All the frequency filters can now be applied to all the file formats, EEG and MEG.
To revert to the previous behavior (saving to native CTF or FIF files, in the database folder), use the menu File > Edit preferences > options "Store continuous files in original folder" and "Save continuous files in original format".
The channel file structure is not copied anymore in the sFile structure used as the descriptor of the continuous files. This information can be read only from the channel file now. Personal scripts might need to be updated to consider this modification.

August 2014

MEG auditory tutorial

A new tutorial proposes a standard pipeline for the complete analysis of a simple oddball paradigm in MEG: MEG auditory tutorial. It presents the workflow in the Brainstorm environment, the equivalent documentation for the FieldTrip environment will be available on the FieldTrip website.

July 2014

New processes

Notch filter: Offered as an alternative when the sinusoid removal doesn't work well
Bandstop filter: Same thing for larger artifacts
Remove linear trend
File > Select files: Get all the files from a specific folder with a process
LCMV Beamformer (HL Chan implementation)

Interface improvements

SSP generic: New options "Average", "Use existing SSP projectors" and "Save average artifact"
Display of the EEG electrodes in the MRI viewer
Time-frequency figures: New option "smooth display"
New figure popup menu: Snapshots > Open as figure
Support for the new Matlab2014b graphics system

June 2014

Resting-state MEG and phase-amplitude coupling

Two new tutorial are available online to explore the cross-frequency coupling in MEG resting state recordings: Resting state MEG and Phase-amplitude coupling

They will allow you to reproduce step-by-step the analysis and the results illustrated in this article:
Canolty RT, Edwards E, Dalal SS, Soltani M, Nagarajan SS, Kirsch HE, Berger MS, Barbaro NM, Knight RT,
High gamma power is phase-locked to theta oscillations in human neocortex
Science, 313(5793):1626-8.

Elekta-Neuromag tutorial

A updated version of the Elekta-Neuromag tutorial is finally available: click here.

May 2014

New processes

Apply montage: To save the result of a custom EEG electrode montage
Surface smoothing: Now supportes time-frequency files in input
Export to SPM: Now supports time-frequency files in input

Other improvements

Display EEG/ECoG/sEEG electrodes in the MRI viewer
MRI Viewer: Allow the direct overlay of two MRI volumes
Spectrum plot: The frequency axis can be displayed using a logarithmic scale
SSP: Create from one time point of recordings
EDF file format: Added the support for multiple Annotation channels

April 2014

Mixed head models

New developements allow more flexible configurations of source models. Now, different brain regions (cortical or subcortical) can be modeled using different constraints. From the Scout tab, select the menu Atlas > New atlas > Source model option. All the scouts present in this atlas can be associated with different source constraints (surface/volume, constrained/free orientation). Then, when computing the head model, select the option "Custom source model".

This work will be soon part of a detailed tutorial showing how to use efficiently sub-cortical atlases for estimating sources in the deeper regions of the brain.

3D scouts

Scouts may now be defined on 3D source grids. Display the volume-based source results in 3D, then use the Scout tab exactly the way you would do it for surface maps.

March 2014

Yokogawa tutorial

A new online tutorial teaches Brainstorm users how to import and process Yokogawa MEG recordings:
Yokogawa/KIT tutorial

New processes

Granger causality spectral
Native support for scouts in all the connectivity functions
Simulation of auto-regressive signals
Simulation of recordings based on scouts time-series
SSP calculation with two inputs for more flexibility

February 2014

EEG and epilepsy

Many features have been added for displaying and processing clinical EEG and invasive measurement data (ECoG and LFPs). These tools are illustrated in a new online tutorial EEG and epilepsy. It is based on a clinical case from the Epilepsy Center at the University Hospital of Freiburg, Germany. The anonymized dataset can be downloaded directly from the Brainstorm download page.

January 2014

Montage interface

The "channel selection" menu and the "EEG average reference" button have been replaced with a more flexible interface to edit montages. Montages can be used to simply select a list of sensors, re-order them in the display or to do more complex operations. The term refers mainly to EEG, to define the referencing system used to display the values recorded on the electrodes: bipolar montages, custom reference electrodes, average reference. See tutorial: Exploring the recordings

Some EEG montages recommended by the American Clinical Neurophysiology Society have been added to the distribution: longitudinal bipolar, transversal bipolar and referential. They are saved in .mon files in the folder brainstorm3/toolbox/sensors/private.

Average reference: SEEG and ECoG

The average reference is now offered in the the list of available montages for EEG, SEEG and ECoG recordings. By default, the average is calculated from all the electrodes and the same value is subtracted everywhere. In some cases, you may be interested in calculating different averages from different subgroups of electrodes: multiple cortical grids or electrodes stripes. To do this, you have two options:

Create a montage manually that defines exactly what are the operations to perform. For instance, if you have 4 electrodes E1..E4 you want to group together, enter four lines, one for each electrode, with this structure: E1: 0.75*E1, -0.25*E2, -0.25*E3, -0.25*E4
The main problem with this approach is that this montage is not used during the source reconstruction procedure. When possible, always consider the second option.
Set the comment of the electrodes to define the groups. Right-click on the channel file > Edit channel file. Select the electrodes of group #1, right-click > Set channel comment. The electrodes with the same comment would be averaged together.

Signal viewer improvements

Flip +/- button: Exchange the direction of the Y axis, useful in clinical EEG
Clone figure: Right-click on the figure > Figure > Clone figure, or open twice the same data file from the popup menu in the database explorer. You can set different montages on the cloned figures, so you can look at the same information in different ways simultaneously.
Shortcut: Go to the next/previous half page (F4 / Shift+F4)
Setting manually time and amplitude resolutions: right-click > Figure > Set axis resolution
Optimized scrolling time

Desktop management

Dealing with multiple figures can be annoying when you review lots of recordings.
The menu "Window layout options" can help you organize all the opened figures in an efficient way. There are four options for the automatic placement of the figures on the screen, and you can also save your own specific working environment with the new menu User setups.
See tutorial: Exploring the recordings

Colormaps

The management of the colormaps has been revamped to include non-symmetrical colormaps. You can now set independently the minimum and the maximum of the figure colorbar. A white marker has also been added to the colorbar when displaying source maps, to indicate the level of the amplitude threshold.
See tutorial: Exploring the recordings

December 2013

Filter files by name or comment

A new filter text box can help you select easily files in the Process1 and Process2 tabs.
See tutorial: Selecting files in the database.

New supported file formats

EEG: Deltamed Coherence-Neurofile (.bin/.txt)
Electrophysiology: NeuroScope / Klusters (.eeg/.dat)

Other improvements

Re-organization of the tabs: now they can be added and removed on demand
Scouts: Remove a vertex from a scout by holding the shift key while clicking
OpenMEEG: Help menu to make it easier to install or update

November 2013

New processes

Simulate > Auto-regressive and custom signals
Simulate > Simulate recordings from scouts (transform matrix files into source files)
Extract > Apply statistic threshold (export stat file with a specific static threshold)
Extract > Unconstrained to flat map (convert unconstrained sources to flat cortical maps)
File > Add tag
File > Select files with tag
Events > Detect analog triggers
Sort event groups by name/by time (Record tab, menu Events)

October 2013

New tutorial: How to write your own plugins

Brainstorm offers a flexible plug-in structure. If you are interested in running your own code from the Brainstorm interface and benefit from the powerful database and visualization systems, the best option is probably for you to create your own process functions.

You would be able to exchange code easily with your collaborators and the methods you develop could immediately reach thousands of users. Once your functions are stable, we can integrate them in the main Brainstorm distribution and maintain the code for you to ensure it stays compatible with the future releases of the software.

Tutorial: How to write your own process

September 2013

Find Brainstorm users next to you

Brainstorm and SPM

It is now very easy to pre-process your recordings and estimate sources in Brainstorm, and do you statistics in SPM8 and SPM12. This powerful combination is illustrated in the following tutorials:
Export volume source maps to SPM8
Export surface source maps to SPM8/SPM12.

August 2013

Using FreeSurfer for the subject coregistration

The FreeSurfer software registers all the subjects to the FSAverage atlas using a spherical representation of the cortex. Each hemisphere of the subject's brain is inflated to a sphere, which is then deformed to match the curvature map of the equivalent sphere in the FSAverage subject.

In the case of a group study, these results are now used by default in Brainstorm to register all the subjects on the same default anatomy. For more information, read the group analysis tutorial.

July 2013

FreeSurfer subcortical atlas and cortical maps

Many news on the FreeSurfer import side. Now Brainstorm imports the subcortical atlas aseg.mgz as a set of surfaces. The cortical thickness results can also be saved in the database and explored easily. More information on the FreeSurfer tutorial page.

New anatomy templates

New models are available to replace the previous Colin27 default anatomy in your Brainstorm protocols. Right-click on (Default anatomy) > Use template. If a package is not available on your system, it will be downloaded from the Brainstorm website and saved in $HOME/.brainstorm/templates. The options available in this menu are:

Colin27: Average of 27 scans of the same head, processed with FreeSurfer 5.3: more information
Colin27_2012: Previous version of the default anatomy distributed with Brainstorm
ICBM152: Non-linear average of 152 subjects, processed with FreeSurfer 5.3: more information
FSAverage: Average of 40 subjects using a spherical averaging described in (Fischl et al. 1999)

MRI segmentation: CIVET

The results of the CIVET anatomical segmentation pipeline, developed at the MNI, can be automatically imported in Brainstorm (surfaces and cortical thickness maps). Right-click on a subject > Import anatomy folder > Select "CIVET folder".

More information: CIVET website and CIVET tutorial.

Join the Brainstorm user community

A new section of the website dedicated to usage statistics and exchange between users: User community.

Brainstorm movie studio

A new fantastic feature to create movies: the "Snapshop > Movie (time): All figures" that you can find on all the 2D and 3D figures. Instead of capturing one figure only, it captures them all and create a movie showing what you see on the screen. Arrange your figures the way you want and create a movie of all your workspace at once.

May 2013

MRI segmentation: BrainSuite support

The results of the BrainSuite anatomical segmentation can be automatically imported in Brainstorm (surfaces and atlases). See: BrainSuite website and BrainSuite tutorial.

New processes

Standardize > Concatenate recordings
Test>StudentT-test: Now available on time-frequency maps
Standardize>Uniform row names: Re-order the signals in a set of files to make them compatible.
Average>Average rows: Average the different signals in a time-frequency file.
Pre-process>Band-pass filter: Now available on source maps
Standardize>Event related perturbation
Events > Add time offset

April 2013

Event markers in the imported recordings

All the time markers available in the continuous recordings are now preserved when importing epochs in the database. It is also possible to add new markers to segment of recordings imported in the database, and to generate new epochs based on them.

A new option of the averaging process allows all the events from all the individual epochs to be combined. It can be a quick way to check that an event of interest (for instance the eye blinks) is not time-locked to the stimulus.

Dynamic Z-score

The Z-score operation, ie. the normalization of the signals by the level of noise calculated over a baseline, now exists in two forms. The process previously called "Compute Z-score" is now available as "Standardize > Z-score (static)".

The new process "Standardize > Z-score (dynamic)" produces the exact same results in terms of display, but calculated in an optimized way. Instead of re-writing the full file with the normalized values, we save only the mean and the standard deviation over the baseline for each signal, and apply the normalization on-the-fly when the file is loaded in memory.

This has almost no impact for the sensor data, but is a great improvement for the source files for which only the inversion kernel is saved. The static Z-score process would rebuild and save the full source matrix [Nsources x Ntime], while the dynamic version can keep the compact formulation of the linear inverse operator [Nsources x Nsensors]. The resulting files are much smaller and faster to open and review.

March 2013

Phase-amplitude coupling

The process "Frequency > Phase-amplitude coupling" offers a new way to explore the interactions between different frequencies. Phase-amplitude coupling (PAC) refers to the modulation of the amplitude of high-frequency oscillations by the phase of low-frequency oscillations. This process identifies in any type of signal the couple of low/high frequencies that maximizes the PAC metric introduced in [Canolty, 2006]:

Canolty RT, Edwards E, Dalal SS, Soltani M, Nagarajan SS, Kirsch HE, Berger MS, Barbaro NM, Knight RT,
"High gamma power is phase-locked to theta oscillations in human neocortex", Science, 313(5793):1626-8.

The process "Frequency > Simulate PAC signals" proposes a model for generating signals with a strong phase-amplitude coupling, for simulation purposes.

Multiple MRI volumes

Two or more MRI volumes can be imported for the same subject, if they have the same size and are properly co-registered. Only the first volume is used as a reference for placing the fiducial points, the additional ones are there for visualization purpose only. This feature can be useful for grouping different sequences (T1/T2), pre-op and post-op scans, regions of interest from fMRI results, or volume-based anatomical atlases.

Process: Run Matlab command

The process "Pre-process > Run Matlab command" is very simple but very powerful. It loads the files in input and run the signals through a piece of Matlab code that you can edit freely. It can extend a lot the flexibility of the Brainstorm pipeline manager, providing an easy access to any Matlab function or script.

CTF/Neuromag dipole estimation

Dipoles localizations from the CTF DipoleFit and Neuromag Xfit software can be imported in the Brainstorm database and displayed on the same figures as cortical maps. See tutorial: Import and visualize dipoles.

February 2013

Intra-cranial EEG

The last version of the OpenMEEG software includes the ability to calculate forward models for cortical grids and intra-cortical electrodes. We integrated these changes to allow the calculation of sources for these two types of implanted electrodes. To be available in the forward and inverse model options, you need to change manually the type of the channels to respectively "SEEG" and "ECOG" (right-click on the channel file > Edit channel file). More tools are coming to visualize the amplitudes and select the position of the electrodes in the MRI viewer. If you are using these features, please cite both Brainstorm and OpenMEEG in your publications (see How to cite Brainstorm and OpenMEEG BEM head model).

Yokogawa/KIT MEG recordings

The Yokogawa/KIT MEG recordings are now supported. They can be visualized, processed and epoched easily, such as any other file format. The reading function is based on the Yokogawa MEG Reader toolbox in Matlab, version 1.4. Supported extensions: .sqd, .con, .mrk, .ave. Some features will be improved shortly, such as the reading of the channel names, the events and the MEG/MRI registration, but the first prototype is fully working.

The events have to be processed manually: link the continuous file to your subject, then run the process "Events > read from channel" on the "Link to raw file". Select the options TTL or RTTL, and type the names of the channels to use as stim channels (example: " null045, null046").

Figure layouts

We are adding some more flexibility to the way the figures are automatically arranged on the screen. You can explore the different options available in the Layout menu. More features to come, including the ability to save custom layouts for the different types of figures.

Save surface snapshot

You can now create a new surface from the one that is displayed in a 3D figure. The exported surface would include all the current modifications: smoothness and resections. Right click on the figure > Snapshot > Save surface.

January 2013

Documentation

Many new step-by-step tutorials are now available, covering the processing and epoching of continuous files, the artifact rejection and the graphical scripting:

?Review continuous recordings and edit markers
?Detect and remove artifacts
?Epoching and averaging
Full analysis with one script

Report viewer: reload a pipeline

A report is generated each time an operation is executed from the Process1 or Process2 tabs, and automatically saved in the user folder ($HOME/.brainstorm/reports). You can browse through all the previous reports for the current protocol using the Report Viewer (File > Report viewer).

The reports can be reloaded easily: the menu "File > Reload last pipeline" selects again all the files that were selected previously, and opens the Pipeline Editor window and selects all the previous processes. The new button "Reload pipeline" in the toolbar of the Report Viewer allows you to reload any of the previously executed operations.

Processing continuous FIF files

Some important pre-processing operations are now available directly on continuous recordings in FIF format (usually Elekta-Neuromag MEG/EEG recordings). The new available processes include: the band-pass filter, the sinusoid removal (notch filter) and the baseline correction.

To process a continuous FIF file: link it to the Brainstorm database (right-click on the subject > Review RAW file), then drag and drop the "Link to raw file" in the Process1 box. Select a process in the Pre-process category. In output, it would create a new native continuous FIF file in the same folder, and also link it into the Brainstorm database. This feature is also available for CTF recordings, and is one of the key elements of our recommended pre-processing pipeline, as illustrated in the tutorial ?Detect and remove artifacts.

Copy of the noise covariance

As explained in the tutorial ?Noise covariance, the best way to estimate the sensors noise for MEG source reconstruction is to use empty room measurements. This implies that you have to import the noise measurements, calculate the noise covariance matrix, and copy it to the other acquisition runs or subjects.

You can use the popup menus "Copy to other conditions" or "Copy to other subjects", directly copy the file to the target condition using File>Copy/Paste, or use the equivalent keyboard shortcuts Ctrl+C / Ctrl+V. All three operations would automatically re-arrange the noise covariance matrix in case the order/number of channels is different for the noise and the target recordings.

MRI registration: joining interactive and automatic methods

The co-registration of the MEG/Polhemus positions with the anatomy of the subject (MRI+surfaces) is not an easy task. We offer three approaches that should be combined to get the best possible results: a first approximation based on three fiducial points (NAS/LPA/RPA), the automatic fit of the Polhemus head shape on the head surface from the MRI, and an rich interface for refining the results manually. The problem of the automatic method is its strong dependance to the initial conditions.

The new button "Refine using head points" in the edition window allows you to fix iteratively the registration: change the position manually, the run the automatic fit again. This solution can help you getting better registration results while we are working on an improved version of the automatic registration that would be less sensitive to the initial alignment.

Subdivide scouts

The FreeSurfer atlases are now automatically imported in Brainstorm. They provide a good starting point for subdividing the cortex surface into anatomical regions, but the corresponding scouts can be too large for many functional applications. Averaging the time series from 600 different sources is likely to blur too much our data, we might lose the effects of interest. We are working subdividing efficiently the regions of these atlases. The first functions developed in this direction are the menus Subdivide atlas and Subdivide selected scouts in the Scout tab. They both perform a clustering of the existing scouts based on anatomical information.

December 2012

FreeSurfer and BrainVISA

Improvements were made for handling FreeSurfer and BrainVISA segmentations. Both software packages generate a tree of folders that contain all the intermediate steps of the reconstruction, the top folder being the subject name or id. It is now possible to import the entire segmentation folders with just one click. Additionally, new menus are available to generate head surfaces from the MRI.
More details: Freesurfer and BrainVISA.

Importing MRI masks

By "MRI masks", we refer to MRI volumes that contain either only 0 and 1 (binary mask) or integer values (labelled atlas). Both type of MRI masks can be imported directly:

as surfaces: Right-click on subject > Import surfaces > Select the file type "Volume mask (all MRI files)". The tesselation is automatically generated by Brainstorm. This works well only in the case of convex envelopes, it is not recommended for complex objects
as scouts: In the Scout tab, menu Atlas > Load atlas > Select the file type "Volume mask (all MRI files)". For each label in the volume, a scout is created, containing all the vertices that are in this region.

New file types supported

GIfTI .gii surface files, used by default in BrainVISA
Curry event files (.cef)

November 2012

Updated topography plots

The rendering of the 2D topography plots is slightly improved, with a new option to set the number of contour lines.

New processes

Standardize > Uniform epoch time: Sets the same time vector for all the input files
Pre-process > Scale values: Multiply the values of one or several sensors by a fixed factor
Average > Average frequency bands: Average values across frequency bands
Extract > Measure from complex values: Apply a function to complex values (typically Morlet or Hilbert coefficients)

Miscelanous

Processing of time-frequency decompositions of source files is now supported (including for the projection on a default anatomy)
Copy-paste operations are extended to most of the files available in the database explorer
All the keyboard shortcuts have been adapted for Mac systems

October 2012

New interface for the scouts

The scouts interface has been redesigned to integrated the logic of atlases, and the classification of each scout in an anatomical region. You are welcome to visit the following tutorials for more information:
?Tutorials/TutScouts
?Tutorials/LabelFreeSurfer

Project sources to an atlas

One of the main problems when dealing with source time series is the size of files. A new process lets you reduce the dimension of your sources by keeping only one value for each scout instead of one value for each vertex: Source > Downsample to atlas. It works well in the case of a set of scouts covering the entire cortex surface, either with a FreeSurfer atlas, or with a random clustering of the surface (menu Atlas>Surface clustering in the Scout tab).

September 2012

Support for Biosemi BDF files

Brainstorm can now import and review native BDF/BDF+ files from Biosemi.

Support for MANSCAN files

Brainstorm can now import and review native MANSCAN EEG files (SAM Technology, Microamp amplifiers): .mbi/.mb2

August 2012

Drive your Polhemus from Brainstorm

For accurate source localization in MEG and EEG with registration to anatomical MRI image volume and efficient head localization in MEG, a 3D digitization solution such as the Polhemus-Fastrak is required. This new, simple Brainstorm feature will help you save time and is efficient for error-checking while digitizing sensor positions and the subject's head shape. See the Digitize tutorial for more information.

June 2012

Graphical batching interface: final version

All the features available from the Brainstorm interface are now also available as "processes", including the import of the data, the artifact cleaning and the source estimation. A full analysis pipeline, starting from the raw continuous file, can be edited graphically and saved as a Matlab script, easy to read an edit. These scripts can now run on distant servers without any user interaction.

The status of all the computations and the information messages that are generated during the execution of an batch script are now saved in detailed reports that can be reviewed as HTML pages, including screen captures of the data for quality control.

See the two tutorials: ?Processes and Automated processing.

April 2012

Matlab 2012a

The compiled version of Brainstorm is now based on Matlab 2012a. It provides more stability and fixes some issues with the Signal Processing Toolbox. However, if you were previously running the stand-alone version of Brainstorm, you may have to install a newer version of the Matlab Compiler Runtime. See the Installation page.

New processes

Events > Combine stim/response: Create new categories of events to group the markers by pairs (stimulus / response)
Standardize > Z-score with two sets of file in input:
1. Compute the variance s and average m of the baseline from files A,
2. Center on m and divide by s all the files B

March 2012

Frequency analysis

The interface for computing and displaying spectrum and time-frequency information has been largely improved. Two new types of windows are available, allowing the display of the time-frequency matrices as [time x amplitude] or [frequency x amplitude] graphs, for one given frequency or time. Four new processes are available, in the Frequency menu:

Fast Fourier Transform (FFT)
Power spectrum density (Welch)
Hilbert transform
Time-frequency (Morlet wavelets)

All these processes can run on any type of time series: recordings, sources, scouts.They all generate complex values, on which we need to apply a function to extract values that can be represented easily. This function can be changed easily after the computation, as a display parameter:

Power: Most common measure to represent the power of a signal for a given frequency bin
Magnitude: Energy of the signal for a frequency bin = sqrt(power)
Log: Convert to decibels (dB) = 10 * log10(power)
Phase: Extract the phase information for a given frequency bin = the angle of the complex value

Improvements made to the continuous viewer

User-defined keyboard shortcuts to create events (keys 1-9)
New buttons and keyboard shortcuts to explore the time series
Bug fix: Automatic positioning of the windows for MacOSX and Linux is now working

February 2012

Artifact removal with SSP

The SSP projectors are now saved in a more sophisticated way, allowing a dynamic selection of the projectors to apply on the recordings.

Co-registration of MEG runs

One of the problems related with the MEG analysis is that the subject's head can move with respect with the sensors during the acquisition. Hence, for the same subject, the position of a given sensor is different for two different runs or two different days of acquisition. We added a process (Standardize > Co-register MEG runs) to compensate for these head movements between acquisition runs, and register all the runs on one fixed head position. For now this process is limited to one head position per run, but we will soon work on using the continuous head localization information to compensate for the head movements at each time point.

Another issue with the data acquisition is the sensors selection: depending on the acquisition system or the day of acquisition, one may end up having lists of channels that do not match across runs or subjects. For instance: there were more auxiliary channels recorded for a few files, or different EEG amplifiers listed the electrodes in a different order. In these cases, it is very difficult to average or compare the information at the sensor level. The new process "Standardize > Uniform list of channels" automatically fixes all these issues by matching the sensors by name in the different files, and makes them compatible in terms on channel names and indices.

January 2012

Import FreeSurfer cortical parcellation

FreeSurfer is one of the many great academic software applications available to perform MRI image analysis. Brainstorm users can now use FreeSurfer to generate surface envelopes of head tissues to generate a model of MEG or EEG sources. Brainstorm now features the possibility to import the labels for regions of the cortex generated by FreeSurfer's analysis, which correspond to the regions of the Desikan-Killiany and Destrieux cortical parcellation atlases. The corresponding surface areas can subsequently be treated as scouts in Brainstorm, and therefore be used as anatomical ROIs to guide the exploration of MEG/EEG source maps.

See tutorial: Use FreeSurfer cortical parcellation

Import Nifti-compressed MRI images

We have added the possibility to import compressed Nifti MR images directly into Brainstorm's MRI Viewer and export MR volumes as Nifti.

Improved user interface for time series visualization

We have added new, convenient features to navigate through trials, time samples and files in your Brainstorm database. Buttons have been added to the main Brainstorm panel and also into the figure window that display time series: navigate through complex data structures with just a click! You can also adjust the amplitude gain using buttons now, or readily set the scale of time-series displays. As always, feedback is always welcome through our forum.

December 2011

Brainstorm on Facebook!

'Like Us' on Facebook to stay in touch:

November 2011

New tools for artifact detection and correction

1) Specific channels can be scanned for automatic detection of ocular and cardiac artifacts from continuous recordings; this feature works best with dedicated control channels (i.e. ECG and EOG),

2) Artifact modeling and attenuation using a signal space projection (SSP) approach.

Stand-alone distribution for Linux and MacOSX

We introduced a new packaging logic for the distribution of Brainstorm executable (i.e., which does require the user to run a Matlab license). The entire set of application files (Matlab scripts and compiled executable) are now integrated in the same unique archive.

The executable is now platform (OS) independent as it has been reduced to a single .jar file created with Matlab's JavaBuilder, that runs on any platform supporting Matlab. To run the stand-alone version of Brainstorm, you just need to install the free, Matlab Compiler Runtime (version 7.16) foryour operating system.

Brainstorm course in Montreal

Part of the Brainstorm development team has moved to theMcConnell Brain Imaging Center at McGill University's Montreal Neurological Institute, in Montreal, Canada. At this occasion, a full-day training session with 70 participants from across Canada has been organized for new users, back-to-back with the first MEG training workshop of the Canada MEG Consortium (see pictures here).

For more training opportunities, visit our Training pages.

May 2011

Brainstorm reference article

Publication of a special issue of the journal Computational Intelligence and Neuroscience:Academic Software Applications for Electromagnetic Brain Mapping Using MEG and EEG, co-edited bySylvain Baillet, Karl Friston & Robert Oostenveld. We encourage Brainstorm users to cite this reference in their publications featuring analyses performed using Brainstorm (see How to cite Brainstorm).

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, 2011. doi:10.1155/2011/879716,pdf]

Improvements in navigating the database

The file manager has been extended to support drag-and-drop and copy-paste operations. Users can now move or copy easily files from a condition or subject entry to another using the mouse, keyboard shortcuts [CTRL+C (copy), CTRL+X (cut) and CTRL+V (paste)], or the File section from the contextual menus from the GUI.

No MRI for your participants?

No worries: Brainstorm can adjust a template anatomy to individual scalp points (MEG) / electrode locations (EEG).

It is now possible to generate pseudo-individual anatomies from a template, for participants for whom the anatomical MRI volume is not available. This operation is possible if digitized head (scalp) points were acquired using a tracking system (e.g., Polhemus Isotrak), which is commonplace in most MEG labs. The default anatomy (volume and surface envelopes) distributed with Brainstorm (MNI/Colin27) can be transformed (warped) to match the subject's scalp points. This is a great cost-saving alternative when individual anatomy is not accessible to investigators (not recommended for accurate, local mapping of the loci of activity though).

See tutorial: Warping default anatomy.

Refine MRI/MEG registration using digitized scalp points

When importing MEG recordings, the registration between the MRI volume and the MEG was formerly based only on three fiducial points only (nasion, left ear, right ear). This approach is known be potentially of poor accuracy. If multiple (>60, typically) scalp points were digitized, the transformation between the MEG's and the MRI's referential can be refined by minimizing the average distance between the scalp surface obtained from MRI and the actual digitized head points.

See tutorial: Review raw recordings.

April 2011

Realistic boundary-element-modeling (BEM) head models for EEG

A new feature has been made available for a more accurate computation of EEG forward models with realistic geometry (strongly recommended). OpenMEEG generates forward models using a symmetric boundary element method that was developed by the INRIA team ATHENA. It considers three realistic layers (scalp, inner skull, outer skull), which can all be generated from the MRI volume using Brainstorm.

See tutorial: BEM head model.

Source estimation in full brain volume

Source models computed in Brainstorm were until now restricted to the cortical surface. To extend the range of analyses made possible with Brainstorm, and to compare Brainstorm's source estimates with these obtained using other software, source models based on dipole grids sampling the entire brain volume can be obtained and reviewed, using the same efficient tools featured in Brainstorm. See tutorial: Volume source estimation.

March 2011

Combined MEG/EEG source reconstruction

The approach to combine concurrent MEG and EEG recordings to obtain a joint source model has been substantially improved.

Display of source maps in MRI volume

Added multiple options to review and visualize source maps using contact sheets and volume smoothing of activity maps. 1) source maps are spatially smoothed after interpolation in the MRI voxels. The size of the smoothing kernel can be configured: right-click on the figure > MRI display; 2) the resulting volumes can be used to create contact sheets along all viewing directions, either in time or across the volume.

See tutorial: ?Source estimation.

December 2010

Statistical inference: correction for multiple comparisons

When displaying the outcome of a t-test, there is now a new tab "stat" that is shown in the main window, which allows to adjust dynamically the type of correction applied to multiple comparisons and the p-value of the test.

Graphical batching interface

A brand new version of the "Process" tab is available. Processing pipelines can now be elaborated in a convivial way, in just a few clicks! You can also save and export your pipeline as Matlab scripts. The processes available are now written as plug-ins: you can contribute your own process and it will automatically list to your menu of available tasks that can be performed on data.

See tutorial: ?Processes.

September 2010

Continuous/RAW file viewer and event editor

Brainstorm can now be used to visualize and process full length continuous/raw files in native format. See tutorial: ?Review raw recordings and edit markers.

Detection of bad trials / bad channels

New process available to detect bad trials or bad trials based on peak-to-peak values. The peak-to-peak threshold can be set by channel type.

Estimation of the noise covariance from continuous files

The interface that computes the noise covariance matrix can be called on continuous recordings. Right-click on link to raw file > Noise covariance.

Import/export protocols and subjects

New menus to help users exchange data easily. A full protocol can be exported as a single zip file (menu File > Export protocol), and then imported in another database (menu File > Load protocol > Load from .zip file). Same thing for a single subject: right-click on the subject > File > Export subject. The subject .zip file is actually a full protocol zip file with only the exported subject, hence it should be loaded as a protocol.

June 2010

Time-frequency

Computation and visualization of time-frequency decompositions of MEG/EEG and source signals using Morlet wavelets. See tutorial: ?Time-frequency.

Brodmann and Tzourio-Mazoyer atlases

Two lists of scouts have been created for the default anatomy (MNI/Colin27), inspired from the atlases of Tzourio-Mazoyer and Brodmann. To access these files: display the cortex surface of the default anatomy, then in the "Scout" tab click on the "Load scouts" button, on the right of the scouts list.

Recordings visualization: 2D Layout

The 2D Layout display for recordings has been re-writen to include many tools: sensors selection, interactive gain change, zoom in time and space... See tutorial: ?Exploring the recordings.

March 2010

Support for Xfit dipoles files

Dipoles localizations from the Neuromag Xfit software can be imported in Brainstorm database and displayed on the same figures as Brainstorm cortical maps. See tutorial: ?Import and visualize dipoles.

Minimum norm solution

Integration of a new minimum norm solution, with more and better tuned parameters. This algorithm is now similar to the one implemented in MNE software.

Januray 2010

Project sources on default anatomy

Any source file estimated for a given surface can be re-projected on another surface. This allows to project sources of individual subjects on the default anatomy to compare subjects. See tutorial: Project sources on default anatomy.

Display channels in columns

The time series can be displayed in columns. The displayed sensors can be edited with an interface similar to the selection editor in MNE software.

December 2009

Automatic updates

Brainstorm is now self-updating. It tests at each startup if your version is older than a month; if so, it downloads a new version. The software can also be updated manually very easily (menu Help > Update Brainstorm).

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+== July 2018 ==
=== Updated dSPM 2018 ===
 * Major modification in "Compute sources [2018]": <<BR>>dSPM values are no longer scaled by number of trials. See [[https://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Averaging_normalized_values|source tutorial]].

=== Interface ===
 * '''Headless mode''': Brainstorm now runs without any rendering capability, allowing the execution of scripts on distant servers and computation clusters that do not have any display attached to them. Adding snapshots to the execution reports is still possible. Start your script with "brainstorm server".

 * '''Custom montage shortcuts''': In the montage editor, shortcuts can now be associated with any montage in the list.

 * '''Stat duration threshold''': Added "Minimum duration" threshold in the stat tab.
 * New montage: "Average reference (L -> R)" for 10-20 EEG caps

=== Anatomy ===
 * BrainSuite: Now reading subcortical structures from the SVReg atlas. See details.
 * OpenMEEG: Switched to version 2.4, which should increase stability and reliablity.

== April 2018 ==
=== Input/output ===
 * Support for g.tec HDF5 files
 * Support for Curry 6-7-8 EEG recordings
 * Support for Muse .csv EEG recordings
 * Montage can be loaded and saved as CSV files

=== ICA cleaning ===
 * Added option: Sort components based on correlation with a channel (EOG, ECG...)
 * Changed reconstruction method: (Winv_good * W_good) => (eye() - Winv_bad * W_bad)

== March 2018 ==
=== SEEG/ECOG ===
 * Updated tools for ECOG (new display options, many bug fixes)
 * New 2DLayout display option
 * Allow simultaneous display of SEEG and ECOG
 * Local average reference: Now available for all the groups of contacts

=== Bug fixes ===
 * All "Filter" processes were replacing the actual data with the "Std" field
 * Added legends to connectivity matrices displayed as images
 * Added support for Matlab 2018a

== February 2018 ==
=== Anatomy ===
 * FreeSurfer: Import the vox2ras matrix from the .mgz MRI files (ignored until now)
 * FreeSurfer: Correct registration of additional .nii files with full FreeSurfer anatomy folders
 * Export NIfTI: Exporting vox2ras transformation to .nii when volume was not initially .nii
 * MRI 3D: New options "Upsample image" to smooth MRI display in 3D figures
 * New option to add the ASEG atlas and the white matter surface to any 3D figure

=== Source modeling 2018 ===
 * New version of the linear inverse models: bug fixes and support for mixed head models
 * Previous models will remain available as "Compute sources 2016"
 * Documentation: [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation|Source estimation tutorial]]

== January 2018 ==
=== Input/output ===
 * Support for the new '''RICOH MEG''' file format
 * Improved BIDS-MEG importer: derivatives folder (FreeSurfer, MaxFilter), acquisition info (_scans.tsv)
 * Fixed EEGLAB reader: Keep events in epochs, allow epochs with multiple event occurrences
 * Keep acquisition dates in the database (DateOfStudy of the brainstormstudy.at files)

=== Processes ===
 * Noise covariance: Match automatically noise covariance with subjects by acquisition date
 * Average: Added option "median"

== November 2017 ==
=== New tutorial: SEEG epileptogenicity maps ===
The tutorial [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity|SEEG epileptogenicity maps]] illustrates all the new features related with SEEG/ECOG: coregistration of MRI and CT scans, placement of depth electrodes in the post-implantation scans, SEEG bipolar montages, display and processing of intracranial recordings, computation of epileptogenicity maps.

{{attachment:epileptogenicity.gif}}

=== Bug fixes ===
 * Matlab 2017b: A bug in isosurface.m caused irregularities in head surfaces
 * More guided protocol creation to avoid user errors and massive deletions of external folders

== October 2017 ==
=== Anatomy ===
 * New options for [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Volume_coregistration|volume coregistration]] of multiple scans of the same subject (MRI/MRI or MRI/CT)<<BR>><<BR>> {{attachment:mri_coreg.gif||width="607",height="167"}}
 * New interface for [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Editing_the_contacts_positions|placing SEEG/ECOG contacts]] in the MRI Viewer <<BR>><<BR>> {{attachment:seeg_edit.gif||width="609",height="171"}}
 * MRI viewer: Various interface improvements (zoom, shortcuts)
 * MRI viewer and MRI-3D: New menu Jump to maximum (shortcut "M")

=== SEEG/ECOG ===
 * Various improvements for handling SEEG/ECOG data: Import menus, montages, display
 * Add event markers on the signals when the event names match the channel names<<BR>><<BR>> {{attachment:raw_chanevt.gif||width="444",height="119"}}

 * New tab [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Guidelines_panel|Guidelines]] for computing epileptogenicity maps<<BR>><<BR>> {{attachment:guidelines.gif||width="599",height="181"}}

== September 2017 ==
=== Elekta: Major workflow changes ===
 * When importing Elekta .fif files, the default acquisition SSP are not applied by default anymore. These SSP projectors were previously always used in Brainstorm for visualization and source estimation. However, they were meant to be used only to review online recordings from the acquisition computer.
 * Now they are still imported but inactive by default. If you want to use them, for instance for backward compatibility purposes, enable them in the window "Select active projectors". If your recordings now look particularly ugly, our advice is to recompute SSP projectors with Brainstorm, rather than using the default acquisition ones.

=== Input/output ===
 * New '''DICOM converter''' (SPM-based): Use menu "Import MRI" and select file format "MRI: DICOM"
 * Export figures to Plotly: [[Tutorials/Plotly|See tutorial]]
 * Export volume grids as .nii
 * Import channel files in .tsv format (IntrAnat)

== August 2017 ==
=== New processes ===
 * Epilepsy > Epileptogenicity maps: [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Epileptogenicity_maps|See tutorial]]
 * Frequency > Time-resolved phase amplitude coupling (tPAC): [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutPac#Time-resolved_PAC_estimation_with_tPAC|See tutorial]]
 * Frequency > FieldTrip: ft_mtmconvol (Multitaper)
 * Connectivity > Phase transfer entropy
 * Artifacts > Undo 4D/CTF noise compensation
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- * New anatomy template: [[http://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy#BrainSuite_templates|USCBrain]]
 * Computation of SPM canonical surfaces (alternative to FreeSurfer/BrainSuite/BrainVISA)
+ * SEEG/ECOG: New option to import sensor positions in '''subject or MNI coordinates'''
 * Computation of SPM canonical surfaces (alternative to FreeSurfer/BrainSuite/BrainVISA)<<BR>><<BR>> {{attachment:spm_canonical.gif||width="546",height="147"}}
 * New anatomy template: [[http://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy#BrainSuite_templates|USCBrain]] <<BR>><<BR>> {{attachment:USCBrain.gif||width="594",height="79"}}
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- * SEEG/ECOG: New option to import sensor positions in subject coordinates
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+ * Optimized reviewing speed: New option "Downsample recordings for faster display"
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