What's next

A roadmap to the future developments of Brainstorm.

Current topics

Documentation

• Merging the 12+3 introduction tutorials to illustrate better the latest developments

Source modeling

• Implementation of a new unified minimum norm/beamformer framework

Functional connectivity

• Significance thresholding of the connectivity matrices

Computation

• Removing the dependence to the Java interface to run in headless mode
• Interacting directly with distributed computing systems

Compatibility

• Reading and writing FieldTrip structures

• Calling FieldTrip functions from the pipeline

• Calling EEGLAB ICA functions for cleaning ocular artifacts in EEG recordings

Recordings

• Nicer 2D topographies, standardized (using FieldTrip .lay files?)

• 2DLayout:
  • Use the same standard positions, too much space between sensors (Recordings + TF)
  • Overlay multiple conditions

  • RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow

• RAW file viewer:
  • Pre-load next page of recordings
  • Events: advanced process for recombining.

  • Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html

• EEG reference/storage:
  • Bad channels specified at the program level (for sites that have permanent bad channels: AS)
• NIRS:
  • Add new data type
  • Display of sensors by pairs oxy/deoxy (red/blue)
• Images of amplitude: [sensor x time], [trial x time], scout: [trial x time]

  • Can be done with Matrix > View as image: extract cluster, concatenate for all trials

• Filtering:
  • Use short FIR filters instead of IIR for bandpass, to limit the ringing

  • Or allow the users to edit the LowStop parameter in bst_bandpass.

• Show easily recordings maximum/values in the file viewer

Interface

• Colormaps:
  • Create a colormap similar to MNE, where extrema are bright
  • Global colormap max: Should get the maximum across all the open files
• Open new windows as tab
• Copy figures to clipboard (with the screencapture function)
• Removing all the CTRL and SHIFT in the keyboard shortcuts

Connectivity

• Thresholding the connectivity matrices
• t-tests on connectivity measures
• Graph view:
  • Does not work on Matlab 2015a
  • Fixed scales for intensity sliders
  • Fix zoom in one region
  • Text bigger
  • Too much data in appdata
  • Re-write using pure Matlab code and smoothed graphics
  • Fixed scales for intensity sliders
  • Add "=" shortcut for having graphs with similar configurations
  • Disable zoom in one region (serious bugs)
• Coherence:
  • Average cross-spectrum instead of concatenating epochs (to avoid discontinuities)
• Granger:
  • Crashes sometimes: improve stability
  • Re-write and optimize code
  • Add progress bar management
• PLV:
  • Add p-values
  • Remove evoked
  • Optimize code
  • Add time integration
  • Unconstrained sources
• PAC:
  • Refine frequency vector of low frequencies
  • How many central frequencies to use in bst_pac?
  • Change filters: no chirplet functions
  • bst_freqfilter: Use nfcomponents like in bst_pac
  • Esther recommended a larger frequency binning of the PAC estimation
• Other metrics:
  • Coherence by bands: bst_coherence_band_welch.m
  • Granger by bands: bst_granger_band.m
  • Inter-trial coherence
• Multi-tapers?

• Tutorial coherence [1xN] : Reproduce FieldTrip results?

Processes

• Distributed processing: Brainstorm that can run without Java
• Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
• Allow processes in Python and Java

• Call FieldTrip functions from pipeline editor

• Optimize opening time for the menu "Add process"
• SSP:
  • Make average the default option

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

  • Show where the attenuation is projected:
    (sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)

• Bandpass:
  • Offer option: bst_bandpass_fft / bst_bandpass_filter
  • Rewrite without the force low-pass filter at Fs/3
  • Show warning when using inappropriate high-pass filter (precision too high)
  • Use FIR filter
• Spectral flattening (John):
  • ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis
• PSD:
  • Rewrite to have the same input as coherence
  • Normalize with the total power (TF/sum(TF,3))

• Remove line noise: http://www.nitrc.org/projects/cleanline

• Interpolate the bad channels
• ICA for cleaning eye movements in EEG low density (SSP don't work well)
• Band-limited power envelope
• Reports:
  • Save as HTML / PDF
  • Do not display the intermediate files
• Pipeline editor:
  • Add loops over subjects/conditions/trial groups
• Time-frequency:
  • Standardize using: diff before calculation + cumsum (checkbox "flatten data")
  • Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  • Display logs as negative
  • 2D Layout in spectrum
  • Make much faster and more memory efficient (C functions coded by Matti ?)
  • TF scouts: should display average of TF maps
• Artifact detection:
  • Detection of bad segments in the RAW files (Beth)
  • Artifact rejection like SPM: if bad in 20%, bad everywhere
  • Test difference between adjacent samples
• 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 head movements
• Resample continuous files

• 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
• Simulation:

  • Fix units in simulation processes => no *1e-9 in "simulate recordings"

  • Use "add noise" process from Hui-Ling (in Work/Dev/Divers)

Database

• Optimize startup speed
• Start Brainstorm without Java (-nodesktop)
• Sort files by comment
• MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.

• Group matrix files => allow to process matrix files by trial types

• Add notes in the folders (text files, visible as nodes in the tree)
• Screen captures: save straight to the database
• Rename multiple files
• Allow matrix files to be attached to other files

Distributed computing

• Options from FieldTrip:

  • Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer

  • Alternative, with less limitations: http://research.cs.wisc.edu/htcondor/

  • Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine

  • Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub

  • Documentation: http://fieldtrip.fcdonders.nl/faq#distributed_computing_with_fieldtrip_and_matlab

• PSOM: http://psom.simexp-lab.org/

Source modeling

• Dipoles:
  • Finish dipole scanning (allow the tab to control multiple figures separately)
  • Dipole fitting: We will not implement non-linear fits, recommended use of dense volume grids
  • panel_dipoles: Doesn't work with multiple figures
  • Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates
• Panel Get coordinates: Add button "find maximum"
• Create scout form maximum: Not available yet for mixed/volume head model.
• Stenroos 2014 paper: Include the following methods

  • Inner and outer skull surfaces generator from FieldTrip (needs SPM, probably not so different from BST)

  • Nolte corrected-sphere model (good model re:Alex)
  • Fast BEM models
• Visualize Beamformer results:
  • Read CTF SAM .svl
  • 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)
  • Stat and connectivity: what to do? (re-send email John+Sylvain)
• Overlapping spheres: improve the estimation of the spheres for the frontal lobes
• Volume grid:
  • Test volume sources with all the subsequent processes (timefreq, stat...)
  • Optimize: 3D display (better than 9x9 cubes)
  • Optimize: vol_dilate (with 26 neighbors)
• Magnetic extrapolation: Do the same thing with EEG
• Noise covariance matrix:
  • Display with figure_image()
  • 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

• EEG Source modeling: Manage references and bipolar montages properly (maybe not necessary)
• MEG source modeling: Do reconstruction only for a subset of sensors for estimating dipoles?
• Processes compute head model and sources: Additional option to set the file comment
• Time-frequency beamformers:
  • Band-pass everything in different frequency bands + Source estimation + TF
  • Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF
• Display volume scouts and surface scouts at the same time
• Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
• BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
• Hui-Ling beamformers:
  • More explanations about what is in NAI and Spatial filters

  • Explain that is this is better to study effects extended in time (Ntime > Nsensors)

  • Group LCMV+MCB
  • Condition LEFT median nerve: very bad results

• Menu Sources > Simulate recordings:

  • Do not close the 3D figures after generating a new file
  • Add a process equivalent to this menu

Anatomy

• Project all sub-cortical structures to default anatomy
• Warping: Scale option has to be fixed, it is currently very unstable
• Scouts:
  • 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
  • Sort scouts by region in process options
• Co-register MRI and CT for electrodes marking in the MRI Viewer
• 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?
• Smooth surface: Fix little spikes to irregularities in the mesh

• Menu head model > Copy to other conditions/subjects (check if applicable first)

• Add cerebellum to default model generated with "Import FS anatomy"
• Add eyes models to attract eye activity

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

    • http://www.adscience.fr/uploads/ckfiles/files/html_files/StatEL/statel_wilcoxon.htm

    • http://www.mathworks.fr/fr/help/stats/signrank.html

    • Less powerful than t-tests
  • 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

• Paired t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo

  • Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test

  • http://fr.wikipedia.org/wiki/Test_de_Shapiro-Wilk

  • http://stats.stackexchange.com/questions/362/what-is-the-difference-between-the-shapiro-wilk-test-of-normality-and-the-kolmog

  • http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html

  • http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html

  • http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab

• Create icons for Stat/PAC, Stat/Sprectrum, etc.
• One sample t-test across subjects

Input / output

• Finish MINC/CIVET integration (finir lecture MINC2: P Bellec)
  • Send email to CIVET mailing list when done

• FieldTrip structures: In / Out (see fieldtrip/utilities/ft_datatype_*)

• EEG File formats:

  • EEG CeeGraph

  • EGI: Finish support for epoched files (formats 3,5,7)
• BCI2000 Input (via EEGLAB plugin)
• EEGLAB import:
  • Selection of conditions in script mode
  • Support for binary AND epoched files (now it's one or the other)
  • Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
• BST-BIN: Add compression
• Review raw on all the file formats (ASCII EEG and Cartool missing)

Distribution & documentation

• Document iEEG in "What's new"
• Rewrite basic 12+3 tutorials: group in one series
  • Illustrate 2D Layout
  • Illustrate unconstrained sources
• Cleaning threads on the forum

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

• Publication list: Fold by years
• Finish existing tutorials:
  • Dipoles
  • Auditory: Extend to MNE/EEGLAB/SPM
  • Auditory: Finish scripts
  • Group MEM/Epilepsy + Epilepsy tutorials
• New tutorials:
  • MEG connectome
  • Scrambled faces (SPM/MNE-Python)
  • Describe all the processes
  • Statistics
  • Coherence (cortico-muscular ?)
  • Intra-cranial recordings (Average ref by groups using Comment field)
  • Co-register MEG runs (Beth)
• Missing in the introduction tutorials:
  • Volume scouts
  • First steps: Brainstorm preferences
  • First steps: Temporary folder
  • Exploration: Clusters
  • Headmodel: explain the fields + how to get the constrained leadfield
  • Sources: Model evaluation (by simulating recordings)
  • Sources: Theshold min. size (not documented yet)
  • Time-frequency: Description of "log freq scale" option
  • Modify a structure manually: Export to Matlab/Import from Matlab
• Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
• Missing in page "Cite Brainstorm": Add all the methods used in the software
• Reference tutorials on Google scholar

• Play videos on wiki with <video> tag (save videos in .ogg)

Current bugs

• Workshops:
  • Create scouts doesn't work: scout created on the other side of the brain
  • Import anatomy folder: Out of memory on Win 32bits (restart Matlab)
  • Compute head model: Out of memory on Win 32bits
  • Bandpass filter: Out of memory (Auditory workshop)
• Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz)
  • Cannot import two .ds folders at once
  • Colors inverted in the PSD/TF plots (power vs. log)
  • Cannot type the name of a channel in "Detect ECG"
• Image viewer: Difficult to get to 100%
• Canolty maps computation: Fix progress bar
• Smooth TF windows that contain multiple plots
• Record tab: Text of epoch number is too big on MacOS
• in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
• 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
• Image viewer has some bugs on some systems
• Screen capture when there is a fading effect in the window manager: captures the window
• Close figure with coherence results should hide the "frequency" slider
• Edit scout in MRI: small modifications cause huge increase of the scout size
• Reports: Text size is too small with Java 1.5 (2006b-2007a)
• Optimize MRI viewer with patch() instead of image()
• Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
• 2DLayout (time series):
  • Sometimes the lines are not visible
  • Does not work when DC offset is not removed
• 2DLayout (TF): Images are too far apart with EEG 20 channels
• Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
• Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG.

Geeky programming details

• Hide Java panels instead of deleting them
• mri2scs: convert arguments to meters
• Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (Matlab 2014b)
• bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
• Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow)
• Optimize bst_get:
  • Now study and subject have necessarily the same folder name
  • Replace big switch with separate functions
• Progress bar:
  • Add different levels (to handle sub-processes)
  • Make work correctly with RAW on resting tutorial
  • Uniformize calls in bst_process/Run
  • Add a "Cancel" button
• Line smoothing / anti-aliasing (time series figures)
• Fix all the 'todo' blocks in the code
• Replace handle "0" with bst_get('groot')
• At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame)
• Error message: Add a link to report directly the bug on the forum

• in_bst_results (isFull=1): DataFile should be relative