What's next

A roadmap to the future developments of Brainstorm.

Current topics

Source modeling

• Implementation of a new unified minimum norm/beamformer framework (work in progress)

Statistics

• Implementation of new parametric and non-parametric tests (work in progress)

Documentation

• Standard workflows for different types of data and experiments (work in progress)

Functional connectivity

• Significance thresholding of the connectivity matrices (not started)

Computation

• Removing the dependence to the Java interface to run in headless mode (not started)
• Interacting directly with distributed computing systems (not started)

Recordings

• 2D topographies:
  • Nicer topographies with circle around 2DDisc (similar to EEGLAB plots)

  • Standardized plots (using FieldTrip .lay files?)

  • Aligned on the midline at least
  • Contour lines sometimes messed up with Elekta recordings
  • Make the surface on which the values are interpolated simpler
• MEG/EEG registration: Apply the same transformation to multiple runs
• 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

  • Same shortcuts as the raw file viewer (right-click + move for gain)
• 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

• Bad channels specified at the program level (for sites that have permanent bad channels: AS)
• 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 (bad for Hilbert as well)

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

• Show easily recordings maximum/values in the file viewer

Interface

• Start Brainstorm without Java (-nodesktop)
• Generalize the user of the units (field .Units): Rewrite processes to save the units correctly
• Colormaps:
  • Manage multiple custom colormaps
  • Allow brightness/contrast manipulations on the custom 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 figures as tab (docked in the Figures window)
• Copy figures to clipboard (with the screencapture function)
• Removing all the CTRL and SHIFT in the keyboard shortcuts
• Display warning before opening files that are too big

Connectivity

• Thresholding the connectivity matrices
• t-tests on connectivity measures
• Check why our Hilbert implementation has huge edge effects
• Connectivity on unconstrained sources: how to group the three orientations?
• Connectivity based on band limited power (Sylvain):
  • Compute Hilbert/Bandpass + correlation of the envelopes
  • Bandpass envelopes before computing correlations?
  • Compute Hilbert(sensors) and then project to source space?
• Multi-tapers?
• Graph view:
  • Does not display negative values correctly (correlation or difference of coherence)
  • Re-write using pure Matlab code and smoothed graphics
  • Fixed scales for intensity sliders
  • Text bigger
  • Too much data in appdata
  • Fixed scales for intensity sliders
  • Add "=" shortcut for having graphs with similar configurations
  • Disable zoom in one region (serious bugs)
  • NxN on sensors: does not place the sensors correctly in space
• Coherence:
  • Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
• Granger:
  • Crashes sometimes: improve stability
  • Re-write and optimize code
  • Add progress bar
• PLV:
  • Add p-values
  • Remove evoked
  • Optimize code
  • Add time integration
  • Unconstrained sources
• PAC:
  • Add input TF , to disconnect TF decomposition and PAC computation (Peter)
  • 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
  • PAC maps: Display all sensors at once (like TF and DynamicPAC)
• Time-resolved correlation/coherence: Display as time bands
• Other metrics:
  • Coherence by bands: bst_coherence_band_welch.m
  • Granger by bands: bst_granger_band.m
  • Inter-trial coherence

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

• Connect NxN: Display as time series > Display warning before trying to open too many signals

Processes

• Edit FieldTrip path in the user preferences

• Optimize pipeline editor speed: Opening the window and the showing menu "Add process" are slow
• ICA:
  • Exploration: Add window with spectral decomposition (useful for muscle artifacts)

  • Comparison JADE/Infomax:
    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135

  • Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)

  • Dimension reduction with PCA adds artifacts: Not done by default in EEGLAB
    Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )
    Student Carl Leichter detailed this in his thesis

  • S Makeig: Use ICA to select the IC of interest instead of only removing artifacts
  • Display of spectrum for components (PSD/FFT)
  • Use FastICA (algo crashing)
  • Understand why EEG/Epilepsy tutorial data crashes if we don't limit the number of components
  • Add components preselection: Correlation with EOG/ECG
  • Import ICA matrices available in EEGLAB .set files
• Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
• Allow processes in Python and Java
• SSP:

  • 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 forced 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 (frequency resolution instead of window length)
  • Allow running on source files attached to continuous files (needs a lot of rewriting)

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

• Band-limited power envelope
• Reports:
  • Save as HTML / PDF
  • Do not display the intermediate files
• Pipeline editor:
  • Add loops over subjects/conditions/trial groups
  • Allow the to stack to Process2 together (file selection + test): Add a number of outputs for each process2 (1 or 2), to know if they can be stacked with another process2
• Time-frequency:

  • Induced calculation: Avg(Power(TF(trials - Avg(Trials)))):
    Add option "Remove evoked response from each trial"

  • Standardize using: diff before calculation + cumsum (checkbox "flatten data")
  • Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  • Display logs as negative
  • Difference of power displayed in log: problems (Soheila)
  • 2D Layout in spectrum
  • Make much faster and more memory efficient (C functions coded by Matti ?)
  • TF scouts: should display average of TF maps
  • Impossible to keep complex values for unconstrained sources
  • Pad short epochs with zero values for getting lower frequencies
  • Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead.
  • 3D figures: Colormaps with "log" option doesn't work
  • Extend clusters tab to display of TF to overlay TF signals (Svet)
  • TF on scouts: Add progress bar when extracting all the scouts time series (can be long)
• Artifact detection:
  • Artifact rejection like SPM: if bad in 20%, bad everywhere
  • Test difference between adjacent samples
  • Allow the detection on differences of signals (bipolar montages)
• 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
• 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)
• Use field process field "Group" to separate Input/Processing/Output options
• Use new Matlab functions: movmean, movsum, movmedian, movmax, movmin, movvar, movstd

Database

• Sort files by comment
• MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
• Matrix files:

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

  • Allow to be dependent from other files
• Add notes in the folders (text files, visible as nodes in the tree)
• Screen captures: save straight to the database
• Rename multiple files
• Default headmodel lost when reloaded: Keep selection on the hard drive (in brainstormstudy.mat)

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

• Mixed head models:
  • Project to templates (scouts or source maps)

  • Create scout form maximum doesn't work (menu Sources > Max value)

  • Display in MRI doesn't work
  • Smooth display: do not smooth subcortical structures
  • Export as .nii volume: doesn't work
• Dipoles:
  • 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"
• Stenroos 2014 paper: Include the following methods

  • Inner and outer skull surfaces generator from FieldTrip (needs SPM)

  • 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:
  • 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

• Beamformers from FieldTrip (LCMV, SAM)

• 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
• 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

• MNI coordinates: Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256)

• Project all sub-cortical structures to default anatomy (check code from Denis S)
• Add cerebellum to default model generated with "Import FS anatomy"
• Import MRIs with different resolutions: re-interpolate automatically
• Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
• 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
  • Display scouts in a tree: hemisphere, region, subregion
  • Downsample to atlas: allow on timefreq/connect files
  • Sort scouts by region in process options

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

• Generate mixed density surfaces
• Optimize computation interpolation MRI-surface (tess_tri_interp)
• Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
• Major bug when importing surfaces for an MRI that was re-oriented manually
• Smooth surface: Fix little spikes to irregularities in the mesh
• Add eyes models to attract eye activity

ECOG/SEEG

• Co-register MRI and CT for electrodes marking in the MRI Viewer
• Import/export electrodes positions in MNI/SCS/MRI coordinates
• Display SEEG+ECOG contacts at the same time

• Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned

Statistics

• t-test/diff_mean between trial groups: better file comments
• 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

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

  • Waiting for test from Dimitrios
  • 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

• Stat FieldTrip: impossible to do Abs(Mean(Sources)) => Is it a problem?

• Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter

• PLS: Partial Least Squares
• In Stat tab: Correction by temporal extension (display only if effect longer than a given input in ms)

Input / output

• FieldTrip structures: Import/Export continuous recordings and non-averaged trials.

• EEG File formats:

  • EEG CeeGraph

  • EGI: Finish support for epoched files (formats 3,5,7)
• BCI2000 Input (via EEGLAB plugin)
• EEGLAB import:
  • 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)
• gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.
• Use new Matlab functions readtable/writetable (2006b): for Excel and text files

Distribution & documentation

• Reference tutorials on Google scholar + ResearchGate

• Cleaning threads on the forum

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

• Finish existing tutorials:
  • EEG/Epilepsy: Rewrite scripts + update contents (with Geneva2015 walkthrough)
  • Dipoles
  • Auditory: Finish scripts
  • Group MEM/Epilepsy + Epilepsy tutorials
• New tutorials:
  • MEG connectome
  • Scrambled faces (SPM/MNE-Python)
  • Coherence (cortico-muscular ?)
  • Intra-cranial recordings
  • Co-register MEG runs (Beth)
• Missing in the introduction tutorials:
  • Volume scouts
  • Sources: Model evaluation (by simulating recordings)
  • Time-frequency: Description of "log freq scale" option
  • Modify a structure manually: Export to Matlab/Import from Matlab
  • File manipulation: file_short, file_fullpath, in_bst_*...
  • Description of all fields in MRI and surfaces
• Script tutorials: ask what folder contains the tutorial datasets
• Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
• Missing in page "Cite Brainstorm": Add all the methods used in the software

Current bugs

• Screen capture:
  • Bug on Win8/Win10: doesn't capture the correct part of the screen
  • Window managers with fading effect: captures the top window
• Image viewer:
  • Difficult to get to 100%
  • Buggy on some systems
• 2DLayout:
  • (TF) Images are too far apart with EEG 20 channels
  • (time series) Sometimes the lines are not visible
  • (time series) Does not work when DC offset is not removed
• Progress bar:
  • Doesn't close properly on some Linux systems
  • Focus requests change workspace when processing constantly (Linux systems)
• MacOS bugs:
  • Buttons {Yes,No,Cancel} listed backwards
  • Record tab: Text of epoch number is too big
  • Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
• Matlab bugs:
  • Interface looks small on screens with very high resolutions: Reduce the resolution
  • Out of memory errors on Win 32bits (restart Matlab)
  • Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
• Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG
• in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
• Edit scout in MRI: small modifications cause huge increase of the scout size
• Canolty maps computation: Fix progress bar

Geeky programming details

• Hide Java panels instead of deleting them
• Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)
• bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
• Shared kernels: "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
• 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
• Optimize MRI viewer with patch() instead of image()