= What's next = A roadmap to the future developments of Brainstorm. <> == Current topics == ==== Source modeling ==== * Implementation of a new unified minimum norm/beamformer framework (work in progress) ==== 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) <
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> == Recordings == * 2D topographies: * Nicer topographies with circle around 2DDisc (similar to EEGLAB plots) * Standardized plots (using FieldTrip .lay files?) * Aligned on the midline at least * Contour lines sometimes messed up with Elekta recordings * Make the surface on which the values are interpolated simpler * MEG/EEG registration: Apply the same transformation to multiple runs * 2DLayout: * Use the same standard positions, too much space between sensors (Recordings + TF) * Overlay multiple conditions * RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow * Same shortcuts as the raw file viewer (right-click + move for gain) * 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 * Option to increase the size of all the elements of the interface (for high res laptop screens) * 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: * 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:<
> 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:<
> * 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: <
> 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 * Allow display of Avg+StdErr * 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 * PSOM: http://psom.simexp-lab.org/ * Various initiatives: http://samirdas.github.io/Data_sharing.html#/ == Source modeling == * Mixed head models: * Create scout form maximum doesn't work (menu Sources > Max value) * Set loose parameter from the interface * Volume grid: * Optimize: 3D display (better than 9x9 cubes) * Optimize: vol_dilate (with 26 neighbors) * Menu Sources > Simulate recordings: * Do not close the 3D figures after generating a new file * Add a process equivalent to this menu * Panel Get coordinates: Add button "find maximum" * Dipoles: * Project individual dipoles files on a template * panel_dipoles: Doesn't work with multiple figures * 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 * 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 * Keep options for inverse computation * OpenMEEG: Post example datasets for the remaining issues: * https://github.com/openmeeg/openmeeg/issues/64 * https://github.com/openmeeg/openmeeg/issues/68 * Example protocol ECOG: doesn't work == 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 * 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) * Reference gradiometers: Keep the orientation of the first or second coil? * Reference gradiometers: Add the sensor definition from coil_def.dat * Validate with phantom 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 * Google Analytics: Create template and update the section of the Community page * New tutorials: * MEG steady-state / high-gamma visual * MEG resting state + OMEGA (Guoimar, Jeremy, Beth) * Intra-cranial recordings (Marcel) * Connectivity: Cortico-muscular coherence * Co-register MEG runs (Beth) * Missing in page "Cite Brainstorm": Add all the methods used in the software * Brainstorm File Exchange: Distribute scripts that users would like to share, but that are too specific to be included in the Brainstorm distribution. => On GitHub * Deface the MRIs of all the tutorials == 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 == 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