What's next

A roadmap for the future developments of Brainstorm.

Next six months

Data acquisition

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

Pre-processing

• Extend processing of continuous CTF files to all file formats
• Continuous viewer: Many small improvements to the usability of its interface
• Improve detection and correction of artifacts with SSP
• Co-registration of several MEG runs on one single head position
• Make all the main operations available in the pipeline editor

File formats

• MRI: MINC
• EEG: Stellate

• EEG: Brain Products / BrainAmp

• Read and display NIRS recordings
• CTF SAM Beamformer results

Functionnal connectivity

• Implementation of methods developed at USC

Recordings

• RAW file viewer:
  • Buttons for changing scales (time + amplitude)
  • Add tooltips to all the buttons / shortcuts
  • Adding events using configurable shortcuts (CTRL+number)
  • If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
  • Documentation: Add definition of bad segments
• RAW processing:
  • Process correctly CTF files saved without the 3rd order grad correction (apply correction before)
  • Allow to overwrite RAW files (but with a HUGE warning)
  • Update file definition + events if time changes (ex: resample)
  • Make it work for the file formats
• Homogenize a selection of several subjects/conditions
  • Popup menu when more than one study selected
  • Creation of a common channel file (match channels by names, not by order)
  • Register MEG runs (recompute fields for a different set of sensors, MEGCoregister from old brainstorm)
• bst_selections:
  • Add user defined combinations of sensors (eg. "double banana" for EEG)
  • Use this to produce "inversed polarity" displayes too (useful in EEG)
  • Standard setups for al the EEG caps
• Intracranial electrodes:
  • Display in the MRI viewer
  • Different data type
  • Display time series
• Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)

Processes

• SSP:
  • Make SSP projections dynamic, and keep the full list instead of always them combining them
  • Take the bad channels in account in the application of the SSP
  • Refresh display after changing the list of bad channels (imported files + raw) so the SSP are applied correctly
  • When processing multiple files: waitbar is all messed up
  • Tune parameters for the automatic detection of heartbeats and eye blinks
  • Write documentation
• Complete processing pipeline:
  • Import + pre-process
  • Sources / head model / noise covariance
  • Project sources
  • Do not generate errors, stay silent and generate a report log that is shown at the end
  • Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions)
• Average:
  • Remember how many trials were used per channel
  • By subject AND condition
• Time-frequency:
  • Write script for timefreq tutorial
  • Make much faster and more memory efficient (C functions coded by Matti ?)
  • Power spectrum: computation (FFT/welch, or average of TF) + display(f/Power, 2DLayout)
  • Display stat computed on time-frequency data
  • Display TF maps separately for the two gradiometers (if not: overlap)
  • Source reconstruction by frequency bands
  • Scouts on surface / time-freq
• Process selection interface:
  • Do not reload the list a each display, but once when starting Brainstorm
  • Popup menus: Add a "Process" menu with all the available processes
  • Bug when redimensioning window (with more than one process)
  • isAvgRef: warning quand process necessite des donnees en AVG REF en entree
  • Save "freqband" option when edited from custom processes
• Other processes:
  • Moving average
  • Remove linear trend
  • Power line removal
  • Bug: gradnorm crashes with bad channels
  • Spatial smoothing: check / document parameters
  • Sinusoid removal: fix new function

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

Database

• 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

• 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
  • Optimize bst_extrapm.m, add waitbar
  • Use the noise covariance from the database instead of recomputing it
• 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:
  • 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)

Anatomy

• BEM surfaces:
  • Fix the bumps at the back of the head
  • Surface edges: same color as the surface when color was changed
• 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
• Atlas:

  • Use BrainVISA / FreeSurfer labeling automatically when importing cortex surface

  • Finalize Brodmann scouts

  • Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND

• 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

• EEG File formats:
  • Stellate

  • BrainVision / BrainAmp: Get functions from EEGLAB

  • Nihon Kohden
  • EDF+

  • EEG CeeGraph

  • NEUROFILE = COHERENCE EEG/video LongTerm Monitoring => Manfred Spueler

  • EGI: Finish support for epoched files (formats 3,5,7)
• Other file formats
  • MEG160 (KIT)

  • CTF: Read STIM channel and generate MarkerFile

  • EEGLAB: Apply ICA matrices, get number of trials for AVG files

  • FieldTrip structures: In / Out

  • Gzipped Nifti (new BrainVISA standard)
  • Output for all the channel file formats
  • Analyze / Nifti:
    • Fix output function (output MRIs cannot be imported in SPM)
    • Use correctly field "orient" to align automatically MRI when importing
• Define scouts from SPM / Analyze 3D masks

• Files > 2Gb: display warnings

Distribution & documentation

• Version with big fonts for live demos

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

• List of all the keyboard and mouse shortcuts
• Send emails to registered users to anounce major improvements
• Script tutorials:
  • Update them to reflect all the recent changes
  • Script for the time-frequency computation
• 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)
  • Scouts: Atlases of Tzourio-Mazoyer and Brodman
  • Processes: Describe all the processes
  • Processes: How to write your own processes (user folder for processes)
  • Processes: Processing RAW files
  • Import raw recordings: Add "detect bad trials/channels" in the pipeline
• Advanced tutorials:
  • MNE sample dataset
  • EEG (How to import an EEG cap)

  • MRI segmentation with FreeSurfer => David Wheland

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

• Display the "What's new" page after downloading new version of brainstorm
• Ask users to send their channel files, align on Colin, distribute

Geeky programming details

• OpenGL options: {none, software, hardware}
• Bug: Scout without overlay, adapt scale for each graph when "Uniformize" 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)
• Double-click doesn't work well on some Linux workstations
• Bug: Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)

• Bug node selection: click on sources > TF: select node-source, not node-condition

• 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)...

• sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way

• 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