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A roadmap for the future developments of Brainstorm. == Next six months == ==== Data acquisition ==== * Improve the acquisition of the head points and the registration MEG / MRI ==== 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 == ==== Documentation ==== * New online tutorials (work in progress: http://neuroimage.usc.edu/brainstorm/TutorialsNew) ==== 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) ==== Compatibility ==== * Reading and writing FieldTrip structures (work in progress) * Calling FieldTrip functions from the pipeline (work in progress) |
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== Details of those features == * SSP: * 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 |
== Recordings == * Nicer 2D topographies, standardized (using FieldTrip .lay files?) * 2DLayout: * Use the same standard positions, too much space between sensors (Recordings + TF) * Overlay multiple conditions * RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow * Same shortcuts as the raw file viewer (right-click + move for gain) |
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* 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): * Read CTF SAM .svl * Create new file type in the database * Display as layers in the MRI viewer * 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" |
* 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 == * 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 * Multi-tapers? * Graph view: <<BR>> * 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: * Refine frequency vector of low frequencies * How many central frequencies to use in bst_pac? * Change filters: no chirplet functions * bst_freqfilter: Use nfcomponents like in bst_pac * Esther recommended a larger frequency binning of the PAC estimation * Other metrics: * Coherence by bands: bst_coherence_band_welch.m * Granger by bands: bst_granger_band.m * Inter-trial coherence * Tutorial coherence [1xN] : Reproduce FieldTrip results? == Processes == * 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 * Distributed processing: Brainstorm that can run without Java * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal * Allow processes in Python and Java * Call FieldTrip functions from pipeline editor * Optimize opening time for the menu "Add process" * SSP:<<BR>> * 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 * Normalize with the total power (TF/sum(TF,3)) * Remove line noise: http://www.nitrc.org/projects/cleanline * Interpolate the bad channels * Band-limited power envelope * Reports: * Save as HTML / PDF * Do not display the intermediate files * Pipeline editor: * Add loops over subjects/conditions/trial groups * Time-frequency: * Standardize using: diff before calculation + cumsum (checkbox "flatten data") * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...) * Display logs as negative * 2D Layout in spectrum * Make much faster and more memory efficient (C functions coded by Matti ?) * TF scouts: should display average of TF maps * Artifact detection: * Detection of bad segments in the RAW files (Beth) * Artifact rejection like SPM: if bad in 20%, bad everywhere * Test difference between adjacent samples * Allow the detection on differences of signals (bipolar montages) |
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* 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) |
* Save standard deviation * Display standard deviation as a halo around the time series * Co-registration of MEG runs: * SSP: Group projectors coming from different files * Finish validation of the method * Apply to continuous recordings for correcting head movements * Resample continuous files * Current Source Density (CSD) => Ghislaine<<BR>>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html * Other processes: * Moving average * Max * Median * Significance test (Dimitrios, Leo) * Spatial smoothing: check / document parameters * Contact sheets & movies: use average of time windows instead of single instants, for each picture. * Optical flow * Simulation: * Fix units in simulation processes => no *1e-9 in "simulate recordings" * Use "add noise" process from Hui-Ling (in Work/Dev/Divers) == Database == * Optimize startup speed * Start Brainstorm without Java (-nodesktop) * Sort files by comment |
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* 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) |
* Group matrix files => allow to process matrix files by trial types |
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* Screen captures: save straight to the database * Rename multiple files * Allow matrix files to be attached to other files == Distributed computing == * Options from FieldTrip: * Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer * Alternative, with less limitations: http://research.cs.wisc.edu/htcondor/ * Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine * Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub * Documentation: http://fieldtrip.fcdonders.nl/faq#distributed_computing_with_fieldtrip_and_matlab * PSOM: http://psom.simexp-lab.org/ |
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* Dipoles: * Finish dipole scanning (allow the tab to control multiple figures separately) * Dipole fitting: We will not implement non-linear fits, recommended use of dense volume grids * panel_dipoles: Doesn't work with multiple figures * Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates * Panel Get coordinates: Add button "find maximum" * Create scout form maximum: Not available yet for mixed/volume head model. * Stenroos 2014 paper: Include the following methods * Inner and outer skull surfaces generator from FieldTrip (needs SPM, probably not so different from BST) * Nolte corrected-sphere model (good model re:Alex) * Fast BEM models * Visualize Beamformer results: * Read CTF SAM .svl * Display as layers in the MRI viewer |
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* Define as default * Check all the processes |
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* 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 * Time-frequency beamformers: * Band-pass everything in different frequency bands + Source estimation + TF * Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF * Display volume scouts and surface scouts at the same time * Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm) * BEM: Fix unstable results when one vertex is too close from the layers (5mm ?) * Hui-Ling beamformers: * More explanations about what is in NAI and Spatial filters * Explain that is this is better to study effects extended in time (Ntime > Nsensors) * Group LCMV+MCB * Condition LEFT median nerve: very bad results * Menu Sources > Simulate recordings: * Do not close the 3D figures after generating a new file * Add a process equivalent to this menu |
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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. * Major bug when importing surfaces for an MRI that was re-oriented manually * 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 |
* Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned * Project all sub-cortical structures to default anatomy * Warping: Scale option has to be fixed, it is currently very unstable * Scouts: * Display edges in the middle of the faces instead of the vertices * Project scouts betweens subjects and between hemispheres * Display scouts in a tree: hemisphere, region, subregion * Downsample to atlas: allow on timefreq/connect files * Sort scouts by region in process options * Co-register MRI and CT for electrodes marking in the MRI Viewer * Generate mixed density surfaces * Import / registration: * Major bug when importing surfaces for an MRI that was re-oriented manually * Use mid-gray instead of pial surface? * Smooth surface: Fix little spikes to irregularities in the mesh * Menu head model > Copy to other conditions/subjects (check if applicable first) * Add cerebellum to default model generated with "Import FS anatomy" * Add eyes models to attract eye activity |
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* http://www.adscience.fr/uploads/ckfiles/files/html_files/StatEL/statel_wilcoxon.htm * http://www.mathworks.fr/fr/help/stats/signrank.html * Less powerful than t-tests |
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* Maris, Eric & Oostenveld, Robert. "Nonparametric statistical testing of EEG-and MEG-data." | |
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== 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 == |
* t-test on volume sources * Paired t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo * Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test * http://fr.wikipedia.org/wiki/Test_de_Shapiro-Wilk * http://stats.stackexchange.com/questions/362/what-is-the-difference-between-the-shapiro-wilk-test-of-normality-and-the-kolmog * http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html * http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html * http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab * Create icons for Stat/PAC, Stat/Sprectrum, etc. * One sample t-test across subjects == Input / output == * Finish MINC/CIVET integration (finir lecture MINC2: P Bellec) * Send email to CIVET mailing list when done * FieldTrip structures: In / Out (see fieldtrip/utilities/ft_datatype_*) |
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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:<<BR>> * Support for binary AND epoched files (now it's one or the other) * Allow epoched files with recordings saved in external files (now external files implies continuous recordings) * BST-BIN: Add compression * Review raw on all the file formats (ASCII EEG and Cartool missing) == Distribution & documentation == * Cleaning threads on the forum * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * Finish existing tutorials: * Dipoles * Auditory: Extend to MNE/EEGLAB/SPM * Auditory: Finish scripts * Group MEM/Epilepsy + Epilepsy tutorials * New tutorials: * MEG connectome * Scrambled faces (SPM/MNE-Python) * Describe all the processes * Statistics * Coherence (cortico-muscular ?) * Intra-cranial recordings (Average ref by groups using Comment field) * Co-register MEG runs (Beth) * Missing in the introduction tutorials: * Volume scouts * Sources: Model evaluation (by simulating recordings) * Sources: Theshold min. size (not documented yet) * Time-frequency: Description of "log freq scale" option * Modify a structure manually: Export to Matlab/Import from Matlab * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm" * Missing in page "Cite Brainstorm": Add all the methods used in the software * Reference tutorials on Google scholar == Current bugs == * Workshops: * Create scouts doesn't work: scout created on the other side of the brain * Import anatomy folder: Out of memory on Win 32bits (restart Matlab) * Compute head model: Out of memory on Win 32bits * Bandpass filter: Out of memory (Auditory workshop) * Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz) * Cannot import two .ds folders at once * Colors inverted in the PSD/TF plots (power vs. log) * Cannot type the name of a channel in "Detect ECG" * Image viewer: Difficult to get to 100% * Canolty maps computation: Fix progress bar * Smooth TF windows that contain multiple plots * Record tab: Text of epoch number is too big on MacOS * in_bst_data_multi: If trials have different sizes, output is random (the one of the first file) * tree_dependencies: sources files, reprojected on default anatomy; If based on data files that are bad trials, they should be ignored by tree_dependencies, and they are not * Image viewer has some bugs on some systems * Screen capture when there is a fading effect in the window manager: captures the window * Close figure with coherence results should hide the "frequency" slider * Edit scout in MRI: small modifications cause huge increase of the scout size * Reports: Text size is too small with Java 1.5 (2006b-2007a) * Optimize MRI viewer with patch() instead of image() * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call * 2DLayout (time series): * Sometimes the lines are not visible * Does not work when DC offset is not removed * 2DLayout (TF): Images are too far apart with EEG 20 channels * Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10 * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG. |
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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 * in_bst_results (isFull=1): DataFile should be relative |
What's next
A roadmap to the future developments of Brainstorm.
Current topics
Documentation
New online tutorials (work in progress: http://neuroimage.usc.edu/brainstorm/TutorialsNew)
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)
Compatibility
Reading and writing FieldTrip structures (work in progress)
Calling FieldTrip functions from the pipeline (work in progress)
Recordings
Nicer 2D topographies, standardized (using FieldTrip .lay files?)
- 2DLayout:
- Use the same standard positions, too much space between sensors (Recordings + TF)
- Overlay multiple conditions
RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
- 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
- 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
- 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:
- Refine frequency vector of low frequencies
- How many central frequencies to use in bst_pac?
- Change filters: no chirplet functions
- bst_freqfilter: Use nfcomponents like in bst_pac
- Esther recommended a larger frequency binning of the PAC estimation
- Other metrics:
- Coherence by bands: bst_coherence_band_welch.m
- Granger by bands: bst_granger_band.m
- Inter-trial coherence
Tutorial coherence [1xN] : Reproduce FieldTrip results?
Processes
- 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
- Distributed processing: Brainstorm that can run without Java
- Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
- Allow processes in Python and Java
Call FieldTrip functions from pipeline editor
- Optimize opening time for the menu "Add process"
SSP:<<BR>>
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
- Interpolate the bad channels
- Band-limited power envelope
- Reports:
- Save as HTML / PDF
- Do not display the intermediate files
- Pipeline editor:
- Add loops over subjects/conditions/trial groups
- Time-frequency:
- Standardize using: diff before calculation + cumsum (checkbox "flatten data")
- Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
- Display logs as negative
- 2D Layout in spectrum
- Make much faster and more memory efficient (C functions coded by Matti ?)
- TF scouts: should display average of TF maps
- Artifact detection:
- Detection of bad segments in the RAW files (Beth)
- Artifact rejection like SPM: if bad in 20%, bad everywhere
- Test difference between adjacent samples
- 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
Current Source Density (CSD) => Ghislaine
http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html- Other processes:
- Moving average
- Max
- Median
- Significance test (Dimitrios, Leo)
- Spatial smoothing: check / document parameters
Contact sheets & movies: use average of time windows instead of single instants, for each picture.
- Optical flow
- Simulation:
Fix units in simulation processes => no *1e-9 in "simulate recordings"
- Use "add noise" process from Hui-Ling (in Work/Dev/Divers)
Database
- Optimize startup speed
- Start Brainstorm without Java (-nodesktop)
- Sort files by comment
- MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
Group matrix files => allow to process matrix files by trial types
- Add notes in the folders (text files, visible as nodes in the tree)
- Screen captures: save straight to the database
- Rename multiple files
- Allow matrix files to be attached to other files
Distributed computing
Options from FieldTrip:
Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer
Alternative, with less limitations: http://research.cs.wisc.edu/htcondor/
Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine
Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub
Documentation: http://fieldtrip.fcdonders.nl/faq#distributed_computing_with_fieldtrip_and_matlab
Source modeling
- Dipoles:
- Finish dipole scanning (allow the tab to control multiple figures separately)
- Dipole fitting: We will not implement non-linear fits, recommended use of dense volume grids
- panel_dipoles: Doesn't work with multiple figures
- Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates
- Panel Get coordinates: Add button "find maximum"
- Create scout form maximum: Not available yet for mixed/volume head model.
- Stenroos 2014 paper: Include the following methods
Inner and outer skull surfaces generator from FieldTrip (needs SPM, probably not so different from BST)
- Nolte corrected-sphere model (good model re:Alex)
- Fast BEM models
- Visualize Beamformer results:
- Read CTF SAM .svl
- Display as layers in the MRI viewer
- Unconstrained sources:
- Compute unconstrained and then project on the normal ?
- Difference and stat should be: norm(A) - norm(B)
- Stat and connectivity: what to do? (re-send email John+Sylvain)
- Overlapping spheres: improve the estimation of the spheres for the frontal lobes
- Volume grid:
- Test volume sources with all the subsequent processes (timefreq, stat...)
- Optimize: 3D display (better than 9x9 cubes)
- Optimize: vol_dilate (with 26 neighbors)
- Magnetic extrapolation: Do the same thing with EEG
- Noise covariance matrix:
- Display with figure_image()
- Storage of multiple noise covariance matrices (just like the head models)
- Always save as full, then at inversion time, we can decide between full, heteroskedastic (diagonal) or homoskedastic (i.i.d, scalar)
Problem of having inividual trials + averages in the condition => Display warning or not?
- Save nAvg in noisecov file, to make it easier to scale to other recordings
When deploying to other conditions: Apply destination SSP (NoiseCov = SSP . NoiseCov . SSP' )
Sources on surface: Display peak regions over time (time = color) => A.Gramfort
- Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise)
Calculate ImagingKernel * Gain for a scout
- EEG Source modeling: Manage references and bipolar montages properly (maybe not necessary)
- MEG source modeling: Do reconstruction only for a subset of sensors for estimating dipoles?
- Processes compute head model and sources: Additional option to set the file comment
- Time-frequency beamformers:
- Band-pass everything in different frequency bands + Source estimation + TF
- Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF
- Display volume scouts and surface scouts at the same time
- Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
- BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
- Hui-Ling beamformers:
- More explanations about what is in NAI and Spatial filters
Explain that is this is better to study effects extended in time (Ntime > Nsensors)
- Group LCMV+MCB
- Condition LEFT median nerve: very bad results
Menu Sources > Simulate recordings:
- Do not close the 3D figures after generating a new file
- Add a process equivalent to this menu
Anatomy
Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned
- Project all sub-cortical structures to default anatomy
- Warping: Scale option has to be fixed, it is currently very unstable
- Scouts:
- Display edges in the middle of the faces instead of the vertices
- Project scouts betweens subjects and between hemispheres
- Display scouts in a tree: hemisphere, region, subregion
- Downsample to atlas: allow on timefreq/connect files
- Sort scouts by region in process options
- Co-register MRI and CT for electrodes marking in the MRI Viewer
- Generate mixed density surfaces
- Import / registration:
- Major bug when importing surfaces for an MRI that was re-oriented manually
- Use mid-gray instead of pial surface?
- Smooth surface: Fix little spikes to irregularities in the mesh
Menu head model > Copy to other conditions/subjects (check if applicable first)
- Add cerebellum to default model generated with "Import FS anatomy"
- Add eyes models to attract eye activity
Statistics
- ANOVA: Use LENA functions
- Output = 1 file per effect, all grouped in a node "ANOVA"
- Display several ANOVA maps (from several files) on one single figure, using a "graphic accumulator", towards which one can send any type of graphic object
- Permutation tests:
- t-test only (wilcoxon? sign-test?): paired, equal var, unequal var
- 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
Maris, Eric & Oostenveld, Robert. "Nonparametric statistical testing of EEG-and MEG-data."
Threshold in time: keep only the regions that are significative for contiguous blocks of time, or over a certain number of time points
=> Process that creates a static representation of a temporal window- t-test on volume sources
Paired t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo
- Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test
http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html
http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html
http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab
- Create icons for Stat/PAC, Stat/Sprectrum, etc.
- One sample t-test across subjects
Input / output
- Finish MINC/CIVET integration (finir lecture MINC2: P Bellec)
- Send email to CIVET mailing list when done
FieldTrip structures: In / Out (see fieldtrip/utilities/ft_datatype_*)
- EEG File formats:
EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
- BCI2000 Input (via EEGLAB plugin)
EEGLAB import:
- Support for binary AND epoched files (now it's one or the other)
- Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
- BST-BIN: Add compression
- Review raw on all the file formats (ASCII EEG and Cartool missing)
Distribution & documentation
- Cleaning threads on the forum
Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
- Finish existing tutorials:
- Dipoles
- Auditory: Extend to MNE/EEGLAB/SPM
- Auditory: Finish scripts
- Group MEM/Epilepsy + Epilepsy tutorials
- New tutorials:
- MEG connectome
- Scrambled faces (SPM/MNE-Python)
- Describe all the processes
- Statistics
- Coherence (cortico-muscular ?)
- Intra-cranial recordings (Average ref by groups using Comment field)
- Co-register MEG runs (Beth)
- Missing in the introduction tutorials:
- Volume scouts
- Sources: Model evaluation (by simulating recordings)
- Sources: Theshold min. size (not documented yet)
- Time-frequency: Description of "log freq scale" option
- Modify a structure manually: Export to Matlab/Import from Matlab
- Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
- Missing in page "Cite Brainstorm": Add all the methods used in the software
- Reference tutorials on Google scholar
Current bugs
- Workshops:
- Create scouts doesn't work: scout created on the other side of the brain
- Import anatomy folder: Out of memory on Win 32bits (restart Matlab)
- Compute head model: Out of memory on Win 32bits
- Bandpass filter: Out of memory (Auditory workshop)
- Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz)
- Cannot import two .ds folders at once
- Colors inverted in the PSD/TF plots (power vs. log)
- Cannot type the name of a channel in "Detect ECG"
- Image viewer: Difficult to get to 100%
- Canolty maps computation: Fix progress bar
- Smooth TF windows that contain multiple plots
- Record tab: Text of epoch number is too big on MacOS
- in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
- tree_dependencies: sources files, reprojected on default anatomy; If based on data files that are bad trials, they should be ignored by tree_dependencies, and they are not
- Image viewer has some bugs on some systems
- Screen capture when there is a fading effect in the window manager: captures the window
- Close figure with coherence results should hide the "frequency" slider
- Edit scout in MRI: small modifications cause huge increase of the scout size
- Reports: Text size is too small with Java 1.5 (2006b-2007a)
- Optimize MRI viewer with patch() instead of image()
- Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
- 2DLayout (time series):
- Sometimes the lines are not visible
- Does not work when DC offset is not removed
- 2DLayout (TF): Images are too far apart with EEG 20 channels
- Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
- Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG.
Geeky programming details
- Hide Java panels instead of deleting them
- 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
in_bst_results (isFull=1): DataFile should be relative