What's next

A roadmap to the future developments of Brainstorm.

Current topics

Data acquisition

• Improve the acquisition of the head points and the registration MEG / MRI

• Real-time processing and display (based on FieldTrip realtime module)

• Support for intra-cranial recordings

Pre-processing

• Correction for head movements (using the continuous head localization coils)

Source modeling

• Computation of equivalent current dipoles
• Display results of CTF SAM beamformer

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

Data management

• Filter the display of the tree by type / name / tag

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
  • 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 cale 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

• Imported recordings: Offer the same interface as the RAW viewer:
  • Scroll bar
  • Events viewer / editor
  • Re-epoch (import from files in database)
  • SSP

• 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)

Connectivity

• Figures: interaction with sensor selection / scouts selections
• Calculation and use of p-values for the metrics
• Trial analysis: Concatenations rather than averages for most metrics
• Optimize bst_coherence
• 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
  • Use little squares
  • Little squares with scout color instead of point
  • Max distance slider: useless
• Event-related coherence?

Processes

• Time-frequency:
  • Stat computed on time-frequency data
  • Validate all the operations on the time-freq files (check for mixed Measures)
  • 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 ?)
• Parallel processing: Use parfor
• Distributed processing:
  • Version of Brainstorm that can run without JAVA
  • Use the BIC/MEG cluster from the pipeline interface (PSOM, P.Bellec)
• 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
  • By subject AND condition
  • 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.

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)

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 ?
  • Define as default
  • Check all the processes
  • 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)
  • Optimize: grid_interp_mri
• Magnetic extrapolation:
  • Do the same thing with EEG
• Project sources:
  • Adapt smooth factor to the number of vertices
  • Number of neighbors to consider = average number of neighbors in the target mesh.
  • Compute by small time blocks
• 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

• Use the FreeSurfer subject co-registration (downsample: keep the correspondance)

• Import / registration:
  • Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...)
  • Auto-reorientation of MRI after selected NAS / LPA / RPA
  • Major bug when importing surfaces for an MRI that was re-oriented manually
• ICBM brain
  • MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab
  • ICBM average surfaces + atlas
  • Using CIVET pipeline for extracting surfaces
• Clustering cortex: Dimitrios, David, Yu-Teng

Statistics

• Stat on scouts / clusters / "matrix"
• 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

Input / output

• MRI: MINC format
• 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)

• FreeSurfer: orig.mgz

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

  • Anatomy: Segmentation with FreeSurfer

  • First steps: Brainstorm preferences
  • Headmodel: explain the fields + how to get the constrained leadfield
  • Coordinate sytems: How to convert between the different coordinates systems in scripts
  • 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

  • How to make and compress a movie (Brainstorm + VirtualDub + XVid)

• Ask users to send their channel files, align on Colin, distribute

Geeky programming details

• Cleaning surfaces: should work with atlases
• Send OpenGL bug report to the Mathworks
• Hide Java panels instead of deleting them
• mri2scs: convert arguments to meters

• Zip files created cannot be open with WinZip

• OpenGL options: {none, software, hardware}
• Bug: Scout without overlay, adapt scale for each graph when "Uniform amplitude" option is unchecked (mixing sources + zscores)
• Waitbars:
  • Replace old waitbars with java ones
  • 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)
• Write shepards.m with new algorithm for nearest neighbors
• Use Matlab Coder to compile / optimize some processes
• Optimize calls to bst_get, now study and subject have necessarily the same folder name