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| A roadmap for the future developments of Brainstorm. == Next six months == ==== Continuous recordings in native format ==== * Extend processing of continuous CTF files to all file formats * Improve detection and correction of artifacts with SSP * Continuous viewer: Many small improvements to the usability of its interface ==== Functionnal connectivity ==== * Implementation of methods developed at USC |
A roadmap to the future developments of Brainstorm. <<TableOfContents(2,2)>> == Current topics == ==== Source modeling ==== * Implementation of a new unified minimum norm/beamformer framework (work in progress) ==== Documentation ==== * Standard workflows for different types of data and experiments (work in progress) * Cross-validation with MNE and FieldTrip: <<BR>>http://martinos.org/mne/dev/auto_tutorials/plot_brainstorm_auditory.html ==== 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) |
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| == New interface elements == | == 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 * Montages: * Separators (" : MLC11" already works, could be just " : "), should add an empty space. * 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) * Add support for montages * RAW file viewer: * Pre-load next page of recordings * Faster display: Downsample time series before plotting * Add field "comment" to markers: For clinicians to add notes (Marcel) * Events: Change the category of a selected event easily, instead of deleting/marking new * Events: Advanced process for recombining.<<BR>>Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html == Interface == * Start Brainstorm without Java (-nodesktop) * Move code to github * Allow FieldTrip functions in compiled version * Generalize the use of the units (field .DisplayUnits): Rewrite processes to save the units correctly * 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...) * Contact sheets & movies: use average of time windows instead of single instants, for each picture. == Connectivity == * Thresholding and stat tests the connectivity matrices * Connectivity on unconstrained sources: how to group the three orientations? * Review by Jan-Mathijs: http://journal.frontiersin.org/article/10.3389/fnsys.2015.00175/full * 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? * 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)<<BR>>Explore inter-trial approaches (Esther refers to chronux toolbox) * Granger: * Crashes sometimes: improve stability * Check for minimum time window (Esther: min around 500-1000 data points) * Re-write and optimize code * Add progress bar * PLV: * Add p-values * Remove evoked * Optimize code * Add time integration * Unconstrained sources * Add warning when running of short windows (because of filters) * 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) * Hui-Ling's PAC: * https://bsp.hackpad.com/Cross-Frequency-Coupling-cChe95lhDHz * https://github.com/NCTU-BSP/MEEG * 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 == * Explore Matlab-Python bridge:<<BR>> https://mail.python.org/pipermail/neuroimaging/2016-June/001001.html * Allow processes in Python and Java * Add FieldTrip functions: * ft_freqanalysis * ft_combineplanar * ft_volumesegment * ft_computeleadfield * ft_prepare_heamodel * Pipeline editor: * Optimize speed: Opening the window and the showing menu "Add process" are slow * Add loops over subjects/conditions/trial groups * PLS: * https://www.rotman-baycrest.on.ca/index.php?section=84 * meg-pls dot weebly dot com * Krishnan 2011: http://www.ncbi.nlm.nih.gov/pubmed/20656037 * Cheung 2015: http://www.sciencedirect.com/science/article/pii/S1053811915007648 * McIntosh 2012: http://www.ncbi.nlm.nih.gov/pubmed/22804773 * McIntosh 2004: http://www.ncbi.nlm.nih.gov/pubmed/15501095 * ICA: * Exploration: Add window with spectral decomposition (useful for muscle artifacts) * Export IC time series (and then compute their spectrum): solves the problem above * 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 * EEGLAB recommends ICA + trial rejection + ICA again: Impossible right now with Brainstorm<<BR>>(http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA) |
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| * Write documentation * 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 * RAW file * 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 |
* 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) * SSS/tSSS: Get implementation from MNE * Bandpass: * Mark with an event the possible edge effects * 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) * Use the progress bar * Remove line noise: http://www.nitrc.org/projects/cleanline * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal * Reports: Click on link reopens exactly the figure * Time-frequency: * Multi-tapers * Short-time Fourier transform: http://www.mikexcohen.com/lectures.html * Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc * Bug: Display logs as negative * Bug: 3D figures: Colormaps with "log" option doesn't work * Bug: 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. * Extend clusters tab to display of TF to overlay TF signals (Svet) * When normalizing with baseline: Propagate with the edge effects marked in TFmask * Allow running TF on montages * Review continuous files in time-frequency space (for epilepsy) * Artifact detection: * Artifact rejection like SPM: if bad in 20%, bad everywhere * Test difference between adjacent samples * Events detection: Add option "std" vs "amplitude" * 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 * Other processes: * Moving average * Max * Median * 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 == * Add buttons to sort files: by name, by comment, by date |
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| * Sources on surface: Display peak regions over time (time = color) => A.Gramfort * 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) * 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) * Interface to compute reaction times based on events: <<BR>>Input:selection of cue event + event response; Output: reation time trial by trial, average, std, distribution... => Etienne Labyt * Database navigator: F4 to switch to next sourcefile * Segmentation in microstates |
* Navigator: Use F2/F3 to explore the entire database (right now F2 works in a weird way) * Matrix files: 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) * protocol.mat can be too big: do not store the results links in it (and recreate when loading) == 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/ * Various initiatives: http://samirdas.github.io/Data_sharing.html#/ |
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| * Inverse: * Stable LCMV Beamformer * MUSIC * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way |
* 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 * Set loose parameter from the interface * Project individual dipoles files on a template * Dipoles: * panel_dipoles: Doesn't work with multiple figures * Panel Get coordinates: Add button "find maximum" * BEM single sphere: Get implementation from MNE * 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 |
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| * 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' ) | * Sources on surface: Display peak regions over time (time = color) => A.Gramfort * Calculate ImagingKernel * Gain for a scout * 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 * Keep options for inverse computation |
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| * MRI import: auto-reorientation of MRI after selected NAS / LPA / RPA. | * MNI coordinates: * Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256) * Compute with FieldTrip: ft_prepare_sourcemodel (linear and non-linear) => Peter * Project all sub-cortical structures to default anatomy (check code from Denis S) * FreeSurfer: * Do not save "mid" surface unless specified explicitely with the process version * 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) * BrainVISA: Add support for MarsAtlas (Guillaume A) * BrainSuite: * Use BrainSuite inner skull for surface generation * Use same colors for left and right for anatomical atlases * 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 == * Important new processes for a full processing pipleline: * Import, and segmentation of RAW files * Detect bad segments on RAW (then events in "bad" segments would be ignored) * Artifact detection: use other things than simple value thresholds (like variance of the sensors...) * Create events list based on thresholds on some channels (Stim, EOG, ECG...) => Etienne Labyt * Creation of SSP vectors (ex: Remove cardiac artifac) * ICA * Integration of Antoine Ducorps methods (everything in the doc of the dataHandler): * Cardiac artifact correction in MEG * PCA correction of ocular artifacts * Interpolation of missing EEG canal * Headmodel / sources / noise cov * Project sources * Delete intermediary files * Processing raw/continuous: * Process non-FIF files (need to convert the header) * Apply SSP + CTF Compensators(only if it useful - maybe create a specific process for that) * Other processes: * 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: * 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 * John's noise cancellation filters * Chain calls of similar processes (ex. bandpass+sin_remove), to avoid reading the full raw files several times |
* Smooth surface: Fix little spikes due to irregularities in the mesh * Add eyes models to attract eye activity * tess_mrimask: Not robust enough to major holes in the brain * Bug: Hide scouts in the preview of the grid for volume head models == ECOG/SEEG == * Contact positions: Import / set / detect * Import/export electrodes positions in MNI/SCS/MRI coordinates * Co-register MRI and CT for electrodes marking in the MRI Viewer<<BR>>=> Mutual information: BrainVISA > Outils > Recalage rigide * Automatic segmentation of CT scans: See project of Rodrigo Paz (Marseille/Timone) * Import from FreeSurfer/FreeView: Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned * Add history: Save modifications and transformations applied to the channel files (Marcel) * ECOG: How to handle cases where not all the grid contacts are in the channel file? (Marcel) * Project contact positions across subjects (Marcel) * Display: * Display SEEG+ECOG contacts at the same time * Better way to represent ECOG strips that are not in contact with the skull (new type?) * SEEG length: count from the most superficial contact * SEEG default view: transparent cortex instead of MRI viewer (Marcel) * ECOG: Project on cortex instead of inner skull, just for display (Marcel) * Color each strip/grid differently * Bad channels: Contacts greyed out instead of ignored (Marcel) * ECOG: Topography display without the 3D coordinates (Marcel) * 2DLayout: Should not try to use the actual position of the sensors, just the grids/strips. * Display time in H:M:S * Alternatives to OpenMEEG: SimBio/FieldTrip? Matti Stenroos? NFT/NIST? * Prepare tutorial with public dataset (Marcel) |
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| * ANOVA: Use LENA functions | * 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 == |
* New process to test for Gaussianity using swtest * PLS: Partial Least Squares * Simulate recordings with specific properties, for stat validation * Quality control before statistics, on condition averages across subjects:<<BR>>mean(baseline)/std(baseline): shows bad subject quickly. * Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter == Input / output == * 4D file format: * Use reader from MNE-Python: mne.io.read_raw_kit (doesn't require Yokogawa slow library) * NYU: Add sensor #6002 (reference magnetometer) * Reference gradiometers: Keep the orientation of the first or second coil? * Reference gradiometers: Add the sensor definition from coil_def.dat * Validate with phatom recordings that noise compensation is properly taken into account * References at too far from the head sensors in Marseille 4D system * The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct * 4D phantom tutorial (JM Badier?) * Export to EDF |
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| * Nihon Kohden * EDF+ * !BrainVision / !BrainAmp: Get functions from EEGLAB * EEG !CeeGraph * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler |
* Nihon Koden * Nicolet EEG: Get from from MNE * EEG CeeGraph |
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| * Other file formats * MEG160 (KIT) * CTF: * Read continuous RAW files split in several .meg4 files ( > 2 Go) * 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) * 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 == Programming details == * 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 |
* 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 * BST-BIN: Add compressionto .bst * BIDS-MEG: Automatic loading of BIDS-structured databases * 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 == * Workflows FieldTrip: http://www.fieldtriptoolbox.org/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip * Reference tutorials on Google scholar + ResearchGate * Cleaning threads on the forum * Update the list of features and link in the Introduction page * Google Analytics: Create template and update the section of the Community page * Finish existing tutorials:<<BR>> * Dipoles * Group MEM/Epilepsy + Epilepsy tutorials * Deface the MRIs of all the tutorials * New tutorials: * MEG steady-state / high-gamma visual * Intra-cranial recordings * MEG connectome (impossible without the head shapes) * Coherence (cortico-muscular ?) * Co-register MEG runs (Beth) * Missing in the introduction tutorials: * SSP: Create projector from any topography figure (right-click > Create SSP) * Description of the .pos files (different folder when in .ds folder or when imported after) * Volume scouts * Time-frequency: Description of "log freq scale" option * Detect bad channels: Peak-to-peak * 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 * (TF) Units are weird with % values * (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling * (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 * 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 * Change of default anatomy does not reset the interpolation matrices in all the subjects. * After projecting sources once from subject to default anat, the interpolation is saved and not updated. Interpolations need to be removed manually before projecting again on a new template. == Geeky programming details == * Hide Java panels instead of deleting them * Processes with "radio" and "radio_line" options: Replace with "radio_label" and "radio_linelabel" * 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)... * Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow) * Rewrite all GUI functions with gui_component * Remove field "!BrainStormSubject" in the studies file: force same folder name for anat & data * Allow protocols with same folder for anat and data * Ensure that all the loaded and saved filenames are in "unix" format * Use parfor: When not available, replace directly all the "parfor" with "for" in file.m * Use Matlab GPU toolbox * Re-use panels instead of delete+create again * Optimize bst_read_events_track * Write shepards.m with new algorithm for nearest neighbors * Use tesselations_stat and tesselations_outwards to clean surfaces * Movies: Use JAVE (Java) * Screen captures: Use Yair Altman functions (in Matlab Central) * Use Matlab Coder to compile / optimize some processes == Distribution & documentation == * Compile stand-alone version: Linux, MacOS * Version with big fonts for live demos * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * 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 == Unsolved problems == * Surfaces: * Influence of the software used to extract surfaces (!BrainVisa, !BrainSuite, !FreeSurfer) * Type of cortex surface to use: grey/white, grey/csf, midsurface ? * How to get good surfaces for BEM ? * Group analysis: * 1) localization on individual brain + interpolation on MNI brain ? * 2) localization directly on MNI brain ? * Normalize amplitudes across different subjects / runs ? * Online documentation of forward and inverse methods |
* 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 * Error message: Add a link to report directly the bug on the forum |
What's next
A roadmap to the future developments of Brainstorm.
Contents
Current topics
Source modeling
- Implementation of a new unified minimum norm/beamformer framework (work in progress)
Documentation
- Standard workflows for different types of data and experiments (work in progress)
Cross-validation with MNE and FieldTrip:
http://martinos.org/mne/dev/auto_tutorials/plot_brainstorm_auditory.html
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)
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
- Montages:
- Separators (" : MLC11" already works, could be just " : "), should add an empty space.
- 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)
- Add support for montages
- RAW file viewer:
- Pre-load next page of recordings
- Faster display: Downsample time series before plotting
- Add field "comment" to markers: For clinicians to add notes (Marcel)
- 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
Interface
- Start Brainstorm without Java (-nodesktop)
- Move code to github
Allow FieldTrip functions in compiled version
Generalize the use of the units (field .DisplayUnits): Rewrite processes to save the units correctly
- 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...)
Contact sheets & movies: use average of time windows instead of single instants, for each picture.
Connectivity
- Thresholding and stat tests the connectivity matrices
- Connectivity on unconstrained sources: how to group the three orientations?
Review by Jan-Mathijs: http://journal.frontiersin.org/article/10.3389/fnsys.2015.00175/full
- 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?
- 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)
Explore inter-trial approaches (Esther refers to chronux toolbox)
- Granger:
- Crashes sometimes: improve stability
- Check for minimum time window (Esther: min around 500-1000 data points)
- Re-write and optimize code
- Add progress bar
- PLV:
- Add p-values
- Remove evoked
- Optimize code
- Add time integration
- Unconstrained sources
- Add warning when running of short windows (because of filters)
- 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)
- Hui-Ling's PAC:
- 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
Explore Matlab-Python bridge:
https://mail.python.org/pipermail/neuroimaging/2016-June/001001.html- Allow processes in Python and Java
Add FieldTrip functions:
- ft_freqanalysis
- ft_combineplanar
- ft_volumesegment
- ft_computeleadfield
- ft_prepare_heamodel
- Pipeline editor:
- Optimize speed: Opening the window and the showing menu "Add process" are slow
- Add loops over subjects/conditions/trial groups
- PLS:
- meg-pls dot weebly dot com
Krishnan 2011: http://www.ncbi.nlm.nih.gov/pubmed/20656037
Cheung 2015: http://www.sciencedirect.com/science/article/pii/S1053811915007648
McIntosh 2012: http://www.ncbi.nlm.nih.gov/pubmed/22804773
McIntosh 2004: http://www.ncbi.nlm.nih.gov/pubmed/15501095
- ICA:
- Exploration: Add window with spectral decomposition (useful for muscle artifacts)
- Export IC time series (and then compute their spectrum): solves the problem above
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
EEGLAB recommends ICA + trial rejection + ICA again: Impossible right now with Brainstorm
(http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA)
- 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)
- SSS/tSSS: Get implementation from MNE
- Bandpass:
- Mark with an event the possible edge effects
- 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)
- Use the progress bar
Remove line noise: http://www.nitrc.org/projects/cleanline
- Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
- Reports: Click on link reopens exactly the figure
- Time-frequency:
- Multi-tapers
Short-time Fourier transform: http://www.mikexcohen.com/lectures.html
Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc
- Bug: Display logs as negative
- Bug: 3D figures: Colormaps with "log" option doesn't work
- Bug: 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.
- Extend clusters tab to display of TF to overlay TF signals (Svet)
- When normalizing with baseline: Propagate with the edge effects marked in TFmask
- Allow running TF on montages
- Review continuous files in time-frequency space (for epilepsy)
- Artifact detection:
- Artifact rejection like SPM: if bad in 20%, bad everywhere
- Test difference between adjacent samples
- Events detection: Add option "std" vs "amplitude"
- 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
- Other processes:
- Moving average
- Max
- Median
- 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
- Add buttons to sort files: by name, by comment, by date
- MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
- Navigator: Use F2/F3 to explore the entire database (right now F2 works in a weird way)
- Matrix files: 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)
- protocol.mat can be too big: do not store the results links in it (and recreate when loading)
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
Various initiatives: http://samirdas.github.io/Data_sharing.html#/
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
- Set loose parameter from the interface
- Project individual dipoles files on a template
- Dipoles:
- panel_dipoles: Doesn't work with multiple figures
- Panel Get coordinates: Add button "find maximum"
- BEM single sphere: Get implementation from MNE
- 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
Sources on surface: Display peak regions over time (time = color) => A.Gramfort
Calculate ImagingKernel * Gain for a scout
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
- Keep options for inverse computation
Anatomy
- MNI coordinates:
Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256)
Compute with FieldTrip: ft_prepare_sourcemodel (linear and non-linear) => Peter
- Project all sub-cortical structures to default anatomy (check code from Denis S)
FreeSurfer:
- Do not save "mid" surface unless specified explicitely with the process version
- 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)
BrainVISA: Add support for MarsAtlas (Guillaume A)
BrainSuite:
Use BrainSuite inner skull for surface generation
- Use same colors for left and right for anatomical atlases
- 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 due to irregularities in the mesh
- Add eyes models to attract eye activity
- tess_mrimask: Not robust enough to major holes in the brain
- Bug: Hide scouts in the preview of the grid for volume head models
ECOG/SEEG
- Contact positions: Import / set / detect
- Import/export electrodes positions in MNI/SCS/MRI coordinates
Co-register MRI and CT for electrodes marking in the MRI Viewer
=> Mutual information: BrainVISA > Outils > Recalage rigide- Automatic segmentation of CT scans: See project of Rodrigo Paz (Marseille/Timone)
Import from FreeSurfer/FreeView: Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned
- Add history: Save modifications and transformations applied to the channel files (Marcel)
- ECOG: How to handle cases where not all the grid contacts are in the channel file? (Marcel)
- Project contact positions across subjects (Marcel)
- Display:
- Display SEEG+ECOG contacts at the same time
- Better way to represent ECOG strips that are not in contact with the skull (new type?)
- SEEG length: count from the most superficial contact
- SEEG default view: transparent cortex instead of MRI viewer (Marcel)
- ECOG: Project on cortex instead of inner skull, just for display (Marcel)
- Color each strip/grid differently
- Bad channels: Contacts greyed out instead of ignored (Marcel)
- ECOG: Topography display without the 3D coordinates (Marcel)
- 2DLayout: Should not try to use the actual position of the sensors, just the grids/strips.
- Display time in H:M:S
Alternatives to OpenMEEG: SimBio/FieldTrip? Matti Stenroos? NFT/NIST?
- Prepare tutorial with public dataset (Marcel)
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
- New process to test for Gaussianity using swtest
- PLS: Partial Least Squares
- Simulate recordings with specific properties, for stat validation
Quality control before statistics, on condition averages across subjects:
mean(baseline)/std(baseline): shows bad subject quickly.Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter
Input / output
- 4D file format:
- Use reader from MNE-Python: mne.io.read_raw_kit (doesn't require Yokogawa slow library)
- NYU: Add sensor #6002 (reference magnetometer)
- Reference gradiometers: Keep the orientation of the first or second coil?
- Reference gradiometers: Add the sensor definition from coil_def.dat
- Validate with phatom recordings that noise compensation is properly taken into account
- References at too far from the head sensors in Marseille 4D system
- The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
- 4D phantom tutorial (JM Badier?)
- Export to EDF
- EEG File formats:
- Nihon Koden
- Nicolet EEG: Get from from MNE
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
- BST-BIN: Add compressionto .bst
- BIDS-MEG: Automatic loading of BIDS-structured databases
- 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
Workflows FieldTrip: http://www.fieldtriptoolbox.org/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip
Reference tutorials on Google scholar + ResearchGate
- Cleaning threads on the forum
- Update the list of features and link in the Introduction page
- Google Analytics: Create template and update the section of the Community page
Finish existing tutorials:
- Dipoles
- Group MEM/Epilepsy + Epilepsy tutorials
- Deface the MRIs of all the tutorials
- New tutorials:
- MEG steady-state / high-gamma visual
- Intra-cranial recordings
- MEG connectome (impossible without the head shapes)
- Coherence (cortico-muscular ?)
- Co-register MEG runs (Beth)
- Missing in the introduction tutorials:
SSP: Create projector from any topography figure (right-click > Create SSP)
- Description of the .pos files (different folder when in .ds folder or when imported after)
- Volume scouts
- Time-frequency: Description of "log freq scale" option
- Detect bad channels: Peak-to-peak
- 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
- (TF) Units are weird with % values
- (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling
- (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
- 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
- Change of default anatomy does not reset the interpolation matrices in all the subjects.
- After projecting sources once from subject to default anat, the interpolation is saved and not updated. Interpolations need to be removed manually before projecting again on a new template.
Geeky programming details
- Hide Java panels instead of deleting them
- Processes with "radio" and "radio_line" options: Replace with "radio_label" and "radio_linelabel"
- 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
- Error message: Add a link to report directly the bug on the forum