= What's next = A roadmap to the future developments of Brainstorm. == Current topics == ==== Documentation ==== * New online tutorials (work in progress) ==== Source modeling ==== * Implementation of a new unified minimum norm/beamformer framework (work in progress) ==== Functional connectivity ==== * Significance thresholding of the connectivity matrices (2016) ==== Computation ==== * Removing the dependence to the Java interface to run in headless mode (not started) * Interacting directly with distributed computing systems (not started) <
><
> == Recordings == * Nicer 2D topographies, standardized (similar to EEGLAB plots, using FieldTrip .lay files?) * 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 * 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: * 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) * 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 * 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? == Processes == * 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 * Normalize with the total power (TF/sum(TF,3)) * 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 * 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 * 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 * Allow the detection on differences of signals (bipolar montages) * 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 * 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 == 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 == 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 * Create scout form maximum doesn't work (menu Sources > Max value) * Display in MRI doesn't work * Smooth display: do not smooth subcortical structures * 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 * 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 == * Bug: Head surface generated with Brainstorm is too large * 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 * 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 == * 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? * PLS: Partial Least Squares == 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. == 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: * 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 * 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 * 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) * Interface looks small on screens with very high resolutions: Reduce the resolution * Out of memory errors on Win 32bits (restart Matlab) * 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) * 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) * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call * 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. * 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()