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| == Next six months == ==== Data acquisition ==== * Improve the acquisition of the head points and the registration MEG / MRI * Real-time processing and display (based on FieldTrip realtime module) * Support for optical recordings: Near-infrared spectroscopy (NIRS) * Support for intra-cranial recordings ==== Pre-processing ==== * Correction for head movements (using the continuous head localization coils) * Extend processing of continuous CTF files to all file formats * Make all the main operations available in the pipeline editor '''Source modeling''' |
== Current topics == ==== Functionnal connectivity ==== * Integration of different metrics to study the brain connectivity: <<BR>>Correlation, coherence, Granger causality, phase locking value * Development of new ways to represent the connectivity between sensors or brain regions ==== EEG / epilepsy / intra-cranial recordings ==== * Full EEG/epilepsy online tutorial * Editing the position of intracranial electrodes in the MRI viewer ==== Source modeling ==== |
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==== Functionnal connectivity ==== * Implementation of methods developed at USC '''Data management''' * Filter the display of the tree by type / name / tag |
* Beamformers ==== Large scale analysis ==== * Parallel processing: Reduce the computation times using the parallel processing toolbox * Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters |
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| * Each RAW viewer window should take a full row of windows (auto-arrange windows) * Adding events using configurable shortcuts (CTRL+number) |
* Pre-load next page of recordings * Allow multiple RAW windows(columns display) * Screen setups: save configuration of windows * Time scale: define in fixed s/mm (like the CTF tools) * Secondary windows: display length of time selection |
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| * Set the amplitude scale for the time series * 2DLayout: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow * EEG reference/storage:<<BR>> * Intracranial electrodes: Define and display in the MRI viewer + 3D figures * Re-reference recordings * 2D topo plots: Display bipolar montages with electrodes positions = average of the two electrodes * Bad locations: indicate with [NaN NaN NaN] instead of [0 0 0] * Location of bipolar electrodes: Save the 2 positions in the channel file, with weights=[1 -1] * Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry |
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| * Process correctly CTF files saved without the 3rd order grad correction (apply correction before) * Allow to overwrite RAW files (but with a HUGE warning) * Update file definition + events if time changes (ex: resample) * Make it work for all the file formats * Imported recordings: Offer the same interface as the RAW viewer: * Scroll bar * Events viewer / editor * Re-epoch (import from files in database) * bst_selections: * Add user defined combinations of sensors (eg. "double banana" for EEG) * Use this to produce "inversed polarity" displayes too (useful in EEG) * Standard setups for all the EEG caps |
* Make it work for all the file formats (at least bandpass filter + sin removal) * Events: advanced process for recombining. Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html * Colormaps: <<BR>> * Create a colormap similar to MNE, where extrema are bright * Import data: * Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files) |
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| * Intracranial electrodes: * Display in the MRI viewer * Different data type * Display time series * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab) * Colormaps: * Create a colormap similar to MNE, where extrema are bright * Grey out the portion of the colorbars not displayed because of the threshold |
* 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 * 2D Layout for multiple conditions == Connectivity == * Inter-trial coherence * Figures: interaction with sensor selection / scouts selections * Display NxN as 1xN * PLV: Add a time integration * Correlation with delays? * Work on progress bars * Circle plot: Display Neuromag sensors |
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| * Time-frequency: * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...) * Scouts values for timefreq on surfaces * How to combine 3 orientations for unconstrained sources * Display logs as negative * 2D Layout in spectrum * Make much faster and more memory efficient (C functions coded by Matti ?) * Smooth display of TF/PAC maps (option) * TF scouts: should display average of TF maps * Bandpass: Show warning when using inappropriate high-pass filter (precision too high) * Artifact detection: * Detection of bad segments in the RAW files * Artifact rejection like SPM: if bad in 20%, bad everywhere * Test difference between adjacent samples * Distributed processing: Brainstorm that can run without Java |
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| * Display warning if changing the ChannelFlag while there is a Projector applied | * Display warning if changing the !ChannelFlag while there is a Projector applied |
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| * Write documentation * Complete processing pipeline:<<BR>> * 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 * Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions) * Delete intermediary files * Complete process of "matrix" file |
* Improve interface for SSP on imported recordings * Define SSP from one time point * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2) |
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| * By subject AND condition | * Save standard deviation * Display standard deviation as a halo around the time series |
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| * SSP: Group projectors coming from different files | |
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| * Apply to continuous recordings for correcting for head movements (using head position coils) * Time-frequency: * Write script for timefreq tutorial * Make much faster and more memory efficient (C functions coded by Matti ?) * 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 * 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 |
* Apply to continuous recordings for correcting head movements * Current Source Density (CSD) => Ghislaine<<BR>>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html |
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| * Detrending | |
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| * Remove linear trend * Power line removal * Bug: gradnorm crashes with bad channels |
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| * Sinusoid removal: fix new function | |
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| * Optical flow * Spectrum figure: use bst_selection |
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| * Filter display of the database explorer (filename, file type, comment...) | |
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| * GUI: Save configuration of windows (per protocol) | * Group matrix files => allow to process matrix files by trial types |
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| * Screen captures: save straight to the database |
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| * 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 |
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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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| * Optimize: grid_interp_mri | |
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| * 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 |
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| * 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) |
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| * 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? |
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| * BEM surfaces: * Fix the bumps at the back of the head * Surface edges: same color as the surface when color was changed |
* Scouts: * Mix constrained/unconstrained/volume sources, using the "Source model" atlas * 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 * Generate mixed density surfaces |
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| * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...) * Auto-reorientation of MRI after selected NAS / LPA / RPA |
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| * ICBM brain * MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab * ICBM average surfaces + atlas * Using CIVET pipeline for extracting surfaces * Atlas: * Brodmann scouts=> Replace with FreeSurfer labels * Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND * Clustering cortex: Dimitrios, David, Yu-Teng |
* Use mid-gray instead of pial surface? |
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| * Stat on scouts / clusters / "matrix" | |
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| * t-test on volume sources * Create icons for Stat/PAC, Stat/Sprectrum, etc. * One sample t-test across subjects |
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| * Use BEM surfaces from !FieldTrip | |
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| * Stellate * !BrainVision / !BrainAmp: Get functions from EEGLAB * Nihon Kohden * EDF+ |
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| * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler | |
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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 * Output for all the channel file formats * Define scouts from SPM / Analyze 3D masks * Files > 2Gb: display warnings |
* !FieldTrip structures: In / Out * BCI2000 Input (via EEGLAB plugin) * Export TF maps to SPM / volumes * EEGLAB import: Selection of conditions in script mode |
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| * Version with big fonts for live demos * Automatic update for binary version * Shortcuts: * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * List of all the keyboard and mouse shortcuts * Equivalents for MacOS * Send emails to registered users to anounce major improvements * Script tutorials: * Update them to reflect all the recent changes * Script for the time-frequency computation |
* Add Help buttons and menus (in popups, dialog windows...) => Links to the website. |
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| * Estimate time to complete each tutorial | * Processes: Describe all the processes |
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| * Anatomy: Segmentation with !FreeSurfer | |
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| * Coordinate sytems: How to convert between the different coordinates systems in scripts | |
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| * 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 |
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| * Temporary folder | |
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| * MNE sample dataset | |
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| * MRI segmentation with !FreeSurfer => David Wheland * How to make and compress a movie (Brainstorm + !VirtualDub + XVid) * Ask users to send their channel files, align on Colin, distribute |
== Current bugs == * Record tab: Text of epoch number is too big on MacOS * Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects) * 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 for reports never works: Find another solution * 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 * Problems growing scouts on merged surfaces (Emily) |
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| * OpenGL options: {none, software, hardware} * Bug: Scout without overlay, adapt scale for each graph when "Uniformize" option is unchecked (mixing sources + zscores) * Waitbars: * Replace old waitbars with java ones * Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process) * Double-click doesn't work well on some Linux workstations * Bug: Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects) * Bug node selection: click on sources > TF: select node-source, not node-condition * Bug tree_dependencies: sources files, reprojected on default anatomy; If based on data files that are bad trials, they should be ignored by tree_dependencies, and they are not |
* Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal * Hide Java panels instead of deleting them * mri2scs: convert arguments to meters |
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| * 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 |
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| * 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 |
* 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 * Line smoothing / anti-aliasing (time series figures) |
What's next
A roadmap to the future developments of Brainstorm.
Current topics
Functionnal connectivity
Integration of different metrics to study the brain connectivity:
Correlation, coherence, Granger causality, phase locking value- Development of new ways to represent the connectivity between sensors or brain regions
EEG / epilepsy / intra-cranial recordings
- Full EEG/epilepsy online tutorial
- Editing the position of intracranial electrodes in the MRI viewer
Source modeling
- Computation of equivalent current dipoles
- Beamformers
Large scale analysis
- Parallel processing: Reduce the computation times using the parallel processing toolbox
- Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters
Recordings
- RAW file viewer:
- Pre-load next page of recordings
- Allow multiple RAW windows(columns display)
- Screen setups: save configuration of windows
- Time scale: define in fixed s/mm (like the CTF tools)
- Secondary windows: display length of time selection
- If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
- Documentation: Add definition of bad segments
- Set the amplitude scale for the time series
2DLayout: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
EEG reference/storage:
- Intracranial electrodes: Define and display in the MRI viewer + 3D figures
- Re-reference recordings
- 2D topo plots: Display bipolar montages with electrodes positions = average of the two electrodes
- Bad locations: indicate with [NaN NaN NaN] instead of [0 0 0]
- Location of bipolar electrodes: Save the 2 positions in the channel file, with weights=[1 -1]
Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry
- RAW processing:
- Make it work for all the file formats (at least bandpass filter + sin removal)
Events: advanced process for recombining. Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
Colormaps:
- Create a colormap similar to MNE, where extrema are bright
- Import data:
- Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files)
- NIRS:
- Add new data type
- Display of sensors by pairs oxy/deoxy (red/blue), overlaid
- 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
- 2D Layout for multiple conditions
Connectivity
- Inter-trial coherence
- Figures: interaction with sensor selection / scouts selections
- Display NxN as 1xN
- PLV: Add a time integration
- Correlation with delays?
- Work on progress bars
- Circle plot: Display Neuromag sensors
Processes
- Time-frequency:
- Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
- Scouts values for timefreq on surfaces
- How to combine 3 orientations for unconstrained sources
- Display logs as negative
- 2D Layout in spectrum
- Make much faster and more memory efficient (C functions coded by Matti ?)
- Smooth display of TF/PAC maps (option)
- TF scouts: should display average of TF maps
- Bandpass: Show warning when using inappropriate high-pass filter (precision too high)
- Artifact detection:
- Detection of bad segments in the RAW files
- Artifact rejection like SPM: if bad in 20%, bad everywhere
- Test difference between adjacent samples
- Distributed processing: Brainstorm that can run without Java
- SSP:
Display warning if changing the ChannelFlag while there is a Projector applied
- When processing multiple files: waitbar is not behaving well
- Improve interface for SSP on imported recordings
- Define SSP from one time point
Show where the attenuation is projected:
(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
- 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
Current Source Density (CSD) => Ghislaine
http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html- Other processes:
- Detrending
- 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
- Spectrum figure: use bst_selection
Database
- 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
Source modeling
- 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
- Dipole fitting
- Visualize Beamformer results (contact Zainab Fatima):
- Read CTF SAM .svl
- Create new file type in the database
- Display as layers in the MRI viewer
- Unconstrained sources:
- Compute unconstrained and then project on the normal ?
- 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:
- Scouts 3D
- Test volume sources with all the subsequent processes (timefreq, stat...)
- Optimize: 3D display (better that 9x9 cubes)
- Optimize: vol_dilate (with 26 neighbors)
- Magnetic extrapolation:
- Do the same thing with EEG
- Noise covariance matrix:
- 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?
Anatomy
- Scouts:
- Mix constrained/unconstrained/volume sources, using the "Source model" atlas
- 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
- 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?
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
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
- Create icons for Stat/PAC, Stat/Sprectrum, etc.
- One sample t-test across subjects
Input / output
- EEG File formats:
EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
FieldTrip structures: In / Out
- BCI2000 Input (via EEGLAB plugin)
- Export TF maps to SPM / volumes
- EEGLAB import: Selection of conditions in script mode
Distribution & documentation
Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
- Introduction tutorials:
- Processes: Describe all the processes
- Clusters
- First steps: Brainstorm preferences
- Headmodel: explain the fields + how to get the constrained leadfield
- Sources: Modelized data
- Sources: theshold min. size (not documented yet)
- Import raw recordings: Add "detect bad trials/channels" in the pipeline
- Temporary folder
- Advanced tutorials:
- EEG (How to import an EEG cap)
Current bugs
- Record tab: Text of epoch number is too big on MacOS
- Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)
- 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 for reports never works: Find another solution
- 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
- Problems growing scouts on merged surfaces (Emily)
Geeky programming details
- Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal
- Hide Java panels instead of deleting them
- mri2scs: convert arguments to meters
- bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
- Shared kernels: do the "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
- Line smoothing / anti-aliasing (time series figures)