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| A roadmap for the future developments of Brainstorm. == Next six months == ==== 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 |
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) |
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| == Details of those features == | == 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: Change the category of a selected event easily, instead of deleting/marking new * 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 * Smooth display from figure_image (ERPimage, raster plot...) == 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 == * 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: <<BR>> 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<<BR>>Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )<<BR>>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 |
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| * 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 * 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) * 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 * 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 * Visualize Beamformer results (contact Zainab Fatima): |
* Display warning if changing the ChannelFlag while there is a Projector applied * Show where the attenuation is projected:<<BR>>(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)))): <<BR>>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: |
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| * Create new file type in the database | |
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| * ICBM brain * MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab * ICBM average surfaces + atlas * Using CIVET pipeline for extracting surfaces == Other new features == * Intracranial electrodes: * Display in the MRI viewer * Different data type * Display time series * Stat on scouts / clusters / "matrix" * Average: * Remember how many trials were used per channel * By subject AND condition * Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions) * GUI: Save configuration of windows (per protocol) * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions. * Sources on surface: Display peak regions over time (time = color) => A.Gramfort * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab) * Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise) * Add notes in the folders (text files, visible as nodes in the tree) == Source modeling == |
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| * Compute unconstrained and then project on the normal ? * Define as default * Check all the processes * Difference and stat should be: norm(A) - norm(B) |
* Stat and connectivity: what to do? (re-send email John+Sylvain) |
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| * Scouts 3D | |
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| * Optimize: 3D display (better that 9x9 cubes) | * Optimize: 3D display (better than 9x9 cubes) |
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| * 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 |
* Magnetic extrapolation: Do the same thing with EEG |
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| * 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? |
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| * When deploying to other conditions: Apply destination SSP (!NoiseCov = SSP . !NoiseCov . SSP' ) | * 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 |
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| * BEM: * Fix the bumps at the back of the head * Surface edges: same color as the surface when color was changed * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...) * Use BrainVISA / FreeSurfer labeling automatically when importing cortex surfaces * MRI import: auto-reorientation of MRI after selected NAS / LPA / RPA. |
* 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 |
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| * Finalize Brodmann scouts * Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND * Clustering cortex: Dimitrios, David, Yu-Teng == 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 * 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 |
* 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 |
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| * ANOVA: Use LENA functions | * t-test/diff_mean between trial groups: better file comments * ANOVA: Use LENA functions(?) |
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| * 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<<BR>> => Process that creates a static representation of a temporal window == Display == * OpenGL options: {none, software, hardware} * Colormap: Set colormap max with right-click + move on the colorbar * Bug: Mixing 2 views MRI/3d, white cuts appear after !SetCurrentFigure * 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) * Contact sheets & movies: use average of time windows instead of single instants, for each picture. == I/O == |
* 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 integration: * Import/Export continuous recordings and non-averaged trials. * Export trials with a trial definition: http://neuroimage.usc.edu/forums/showthread.php?2213 |
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| * Stellate * !BrainVision / !BrainAmp: Get functions from EEGLAB * Nihon Kohden * EDF+ * EEG !CeeGraph * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler |
* EEG CeeGraph |
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| * 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:<<BR>> * 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 |
* 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 |
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| * 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 |
* Hide Java panels instead of deleting them * Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b) |
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| * Testing functions: test_ctf "folder" / test_neuromag "folder" / test "folder" => Alex * 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 == 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 shortcuts * Send email 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 |
* 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() |
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: Change the category of a selected event easily, instead of deleting/marking new
- 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
- Smooth display from figure_image (ERPimage, raster plot...)
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
- 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
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://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 integration:
- Import/Export continuous recordings and non-averaged trials.
Export trials with a trial definition: http://neuroimage.usc.edu/forums/showthread.php?2213
- 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()