= What's next = A roadmap to the future developments of Brainstorm. == Next six months == ==== 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 optical recordings: Near-infrared spectroscopy (NIRS) * Support for intra-cranial recordings ==== Pre-processing ==== * Correction for head movements (using the continuous head localization coils) * Extend processing of continuous CTF files to all file formats ==== 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 ==== * Make all the main operations available in the pipeline editor * 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 <
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> == Recordings == * RAW file viewer: * Pre-load next page of recordings * 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 all the file formats * 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 * 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) * Standard setups for all the EEG caps * Import data: * Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files) * Import average only * Force epochs to be complete (same size for all of them) * NIRS: * Add new data type * Display of sensors by pairs oxy/deoxy (red/blue), overlaid * Intracranial electrodes: * Display in the MRI viewer * Different data type * Display time series * Forward model * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab) == Processes == * Connectivity: * Circle plot for NxN interactions * Synthetize + plot N sources into n ROIs (requires scout saved in the surfaces) * Menu to easily recompute teh sources in ROI form * 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 ?) * Complete processing pipeline:<
> * Do not generate errors, stay silent and generate a report log that is shown at the end * Import + pre-process * Sources / head model / noise covariance * Project sources * Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions) * Delete intermediary files * Complete process of "matrix" file * 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) * Process selection interface: * Do not reload the list a each display, but once when starting Brainstorm * 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 * Max * Median * Significance test (Dimitrios, Leo) * 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 == * 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: * Stocker scouts dans les fichiers de surface * Downsample scouts with surfaces * 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: * 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) == 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: * Brodmann scouts=> Replace with !FreeSurfer labels * 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 == * Use BEM surfaces from !FieldTrip * EEG File formats: * Biosemi * Stellate * Nihon Kohden * EEG !CeeGraph * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring * EGI: Finish support for epoched files (formats 3,5,7) * Other file formats * MEG160 (Yokogawa/KIT) * CTF: Read STIM channel and generate !MarkerFile * !FieldTrip structures: In / Out * Output for all the channel file formats * Define scouts from SPM / Analyze 3D masks * Files > 2Gb: display warnings == Distribution & documentation == * Version with big fonts for live demos * 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 * Advanced tutorials: * EEG (How to import an EEG cap) * How to make and compress a movie (Brainstorm + !VirtualDub + XVid) * Ask users to send their channel files, align on Colin, distribute == Geeky programming details == * 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 "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