What's next

A roadmap to the future developments of Brainstorm.

Current topics

Functionnal connectivity

• Integration of different metrics to study the brain connectivity:
  Correlation, coherence, Granger causality, phase locking value

• Development of new ways to represent the connectivity between sensors or brain regions

EEG / epilepsy / intra-cranial recordings

• New tools for exploring EEG recordings (custom montages, faster viewer)
• Full EEG/epilepsy online tutorial
• Editing the position of intracranial electrodes in the MRI viewer

Source modeling

• Computation of equivalent current dipoles
• Beamformers

Large scale analysis

• Parallel processing: Reduce the computation times using the parallel processing toolbox
• Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters

Recordings

• RAW file viewer:
  • Pre-load next page of recordings
  • Allow multiple RAW windows(columns display)
  • Screen setups
  • Time scale: define in fixed s/mm (like the CTF tools)
  • Secondary windows: display length of time selection
  • If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
  • Documentation: Add definition of bad segments
  • Set the amplidute scale for the time series
  • CTRL+S : Save modifications
• RAW processing:
  • Make it work for all the file formats(at least bandpass filter)

  • Events: advanced process for recombining. Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html

• Improve interface for SSP on imported recordings

• Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry

• Colormaps:

  • Define manually minimum => 3 options: [0,max], [-max,max], [min,max]

  • Create a colormap similar to MNE, where extrema are bright
  • Grey out the portion of the colorbars not displayed because of the threshold
• bst_selections:
  • Add user defined combinations of sensors (eg. "double banana" for EEG)
  • Use this to produce "inversed polarity" displayes too (useful in EEG)
• Import data:
  • Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files)
• NIRS:
  • Add new data type
  • Display of sensors by pairs oxy/deoxy (red/blue), overlaid
• Intracranial electrodes:
  • Define and display in the MRI viewer
• Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)
• 2D Layout for multiple conditions

Connectivity

• Figures: interaction with sensor selection / scouts selections
• Display NxN as 1xN
• Adapt colormaps for correlation (min and max properties)
• PLV: Add a time integration
• Work on progress bars
• Circle plot:
  • Display Neuromag sensors
• Event-related coherence?

Processes

• SImulation: Input as a text with a syntax "scoutname = f1(t) + white_noise(t) + ..."
• Time-frequency:
  • Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  • Scouts values for timefreq on surfaces
  • How to combine 3 orientations for unconstrained sources
  • Display logs as negative
  • 2D Layout in spectrum
  • Make much faster and more memory efficient (C functions coded by Matti ?)
• Distributed processing:
  • Version of Brainstorm that can run without JAVA
• SSP:

  • Display warning if changing the ChannelFlag while there is a Projector applied

  • When processing multiple files: waitbar is not behaving well
• Average:
  • Remember how many trials were used per channel
  • Save standard deviation
  • Display standard deviation as a halo around the time series
• Co-registration of MEG runs:
  • SSP: Group projectors coming from different files
  • Finish validation of the method
  • Apply to continuous recordings for correcting for head movements (using head position coils)

• Current Source Density (CSD) => Ghislaine
  http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html

• Other processes:
  • Moving average
  • Max
  • Median
  • Significance test (Dimitrios, Leo)
  • Spatial smoothing: check / document parameters

• Contact sheets & movies: use average of time windows instead of single instants, for each picture.

• Optical flow

Database

• Filter display of the database explorer (filename, file type, comment...)
• MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
• GUI: Save configuration of windows (per protocol)
• Add notes in the folders (text files, visible as nodes in the tree)
• Screen captures: save straight to the database

Source modeling

• Dipole fitting
• Scouts:
  • Represent border as the middle of the adjacent triangles (to have a full segmentation)
• Visualize Beamformer results (contact Zainab Fatima):
  • Read CTF SAM .svl
  • Create new file type in the database
  • Display as layers in the MRI viewer
• Unconstrained sources:
  • Compute unconstrained and then project on the normal ?
  • Difference and stat should be: norm(A) - norm(B)
• Overlapping spheres: improve the estimation of the spheres for the frontal lobes
• Volume grid:
  • Scouts 3D
  • Test volume sources with all the subsequent processes (timefreq, stat...)
  • Optimize: 3D display (better that 9x9 cubes)
  • Optimize: vol_dilate (with 26 neighbors)
• Magnetic extrapolation:
  • Do the same thing with EEG
• Noise covariance matrix:
  • Storage of multiple noise covariance matrices (just like the head models)
  • Always save as full, then at inversion time, we can decide between full, heteroskedastic (diagonal) or homoskedastic (i.i.d, scalar)

  • Problem of having inividual trials + averages in the condition => Display warning or not?

  • Save nAvg in noisecov file, to make it easier to scale to other recordings

  • When deploying to other conditions: Apply destination SSP (NoiseCov = SSP . NoiseCov . SSP' )

• Sources on surface: Display peak regions over time (time = color) => A.Gramfort

• Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise)

• Calculate ImagingKernel * Gain for a scout

Anatomy

• Scouts:
  • Mix constrained/unconstrained/volume sources, using the "Source model" atlas
  • Display edges in the middle of the faces instead of the vertices
  • Project scouts betweens subjects and between hemispheres
  • Display scouts in a tree: hemisphere, region, subregion
  • Downsample to atlas: allow on timefreq/connect files
• Generate mixed density surfaces
• Import / registration:
  • Major bug when importing surfaces for an MRI that was re-oriented manually
• Use mid-gray instead of pial surface?

Statistics

• ANOVA: Use LENA functions
  • Output = 1 file per effect, all grouped in a node "ANOVA"
  • Display several ANOVA maps (from several files) on one single figure, using a "graphic accumulator", towards which one can send any type of graphic object
• Permutation tests:
  • t-test only (wilcoxon? sign-test?): paired, equal var, unequal var
  • nb permutations ~ 1000
  • maximum statistic over "time" or "time and space"
• Permutations / clustering: cf fieldtrip

  • http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock

  • http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq

• Threshold in time: keep only the regions that are significative for contiguous blocks of time, or over a certain number of time points
  => Process that creates a static representation of a temporal window

• t-test on volume sources
• Create icons for Stat/PAC, Stat/Sprectrum, etc.

Input / output

• EEG File formats:

  • EEG CeeGraph

  • NEUROFILE = COHERENCE EEG/video LongTerm Monitoring

  • EGI: Finish support for epoched files (formats 3,5,7)

• FieldTrip structures: In / Out

• BCI2000 Input (via EEGLAB plugin)

Distribution & documentation

• Shortcuts:

  • Add Help buttons and menus (in popups, dialog windows...) => Links to the website.

  • List of all the keyboard and mouse shortcuts
  • Equivalents for MacOS
• Introduction tutorials:
  • Estimate time to complete each tutorial
  • Clusters
  • First steps: Brainstorm preferences
  • Headmodel: explain the fields + how to get the constrained leadfield
  • Sources: Modelized data
  • Sources: theshold min. size (not documented yet)
  • Processes: Describe all the processes
  • Processes: How to write your own processes (user folder for processes)
  • Import raw recordings: Add "detect bad trials/channels" in the pipeline
  • Temporary folder
  • How to export sources for analysis in SPM
• Advanced tutorials:
  • EEG (How to import an EEG cap)
  • Epilepsy / spike analysis
• Ask users to send their channel files, align on Colin, distribute

Geeky programming details

• Matlab/Java memory leaks
• Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal
• Hide Java panels instead of deleting them
• mri2scs: convert arguments to meters
• Waitbars: Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process)
• Bug: Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)
• Bug tree_dependencies: sources files, reprojected on default anatomy; If based on data files that are bad trials, they should be ignored by tree_dependencies, and they are not
• bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
• Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)...
• Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow)
• Optimize calls to bst_get, now study and subject have necessarily the same folder name
• Stat files: store tmap or pmap, not both
• Progress bar with different levels (to handle sub-processes)
• Progress bar: make work correctly with RAW on resting tutorial
• Sort scouts by region
• Force use of javaObjectEDT everywhere (java_create.m)
• Line smoothing / anti-aliasing (time series figures)