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A to-do list for the development of Brainstorm in the next few years == New interface elements == * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions. * Functionnal connectivity (display: see eConnectome) * SSP: * Make SSP projections dynamic, and keep the full list instead of always them combining them * Take the bad channels in account in the application of the SSP * Refresh display after changing the list of bad channels (imported files + raw) so the SSP are applied correctly |
A roadmap to the future developments of Brainstorm. == 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 '''Source modeling''' * Computation of equivalent current dipoles * Display results of CTF SAM beamformer ==== 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 '''Data management''' * Make all the main operations available in the pipeline editor * Filter the display of the tree by type / name / tag '''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 <<BR>><<BR>><<BR>> == Recordings == * RAW file viewer: * Adding events using configurable shortcuts (CTRL+number) * If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations" * Documentation: Add definition of bad segments * RAW processing: * Process correctly CTF files saved without the 3rd order grad correction (apply correction before) * Allow to overwrite RAW files (but with a HUGE warning) * Update file definition + events if time changes (ex: resample) * Make it work for 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) * SSP * Colormaps: * Define manually minimum => 3 options: [0,max], [-max,max], [min,max] * Create a colormap similar to MNE, where extrema are bright * Grey out the portion of the colorbars not displayed because of the threshold |
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* Standard setups for al the EEG caps * 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) |
* Standard setups for all the EEG caps * Import data: * Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files) * Import average only * Force epochs to be complete (same size for all of them) * NIRS: * Add new data type * Display of sensors by pairs oxy/deoxy (red/blue), overlaid * Intracranial electrodes: * Display in the MRI viewer * Different data type * Display time series |
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* 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 |
== Processes == * Connectivity: * Circle plot for NxN interactions * Synthetize + plot N sources into n ROIs (requires scout saved in the surfaces) * Menu to easily recompute teh sources in ROI form * Time-frequency: * Stat computed on time-frequency data * Validate all the operations on the time-freq files (check for mixed Measures) * 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 ?) * Complete processing pipeline:<<BR>> * Do not generate errors, stay silent and generate a report log that is shown at the end * Import + pre-process * Sources / head model / noise covariance * Project sources * Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions) * Delete intermediary files * Complete process of "matrix" file * Parallel processing: Use parfor * Distributed processing: * Version of Brainstorm that can run without JAVA * Use the BIC/MEG cluster from the pipeline interface (PSOM, P.Bellec) * SSP: * Display warning if changing the !ChannelFlag while there is a Projector applied * When processing multiple files: waitbar is not behaving well * Average: * Remember how many trials were used per channel * By subject AND condition * 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 for head movements (using head position coils) * 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 * Other processes: * Moving average * Max * Median * Significance test (Dimitrios, Leo) * Remove linear trend * Power line removal * Bug: gradnorm crashes with bad channels * Spatial smoothing: check / document parameters * Sinusoid removal: fix new function * Contact sheets & movies: use average of time windows instead of single instants, for each picture. == Database == * Filter display of the database explorer (filename, file type, comment...) * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions. * GUI: Save configuration of windows (per protocol) * Add notes in the folders (text files, visible as nodes in the tree) |
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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 |
* Dipole fitting * Scouts: * Stocker scouts dans les fichiers de surface * Downsample scouts with surfaces * Visualize Beamformer results (contact Zainab Fatima): * Read CTF SAM .svl * Create new file type in the database * Display as layers in the MRI viewer |
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* Compute unconstrained and then project on the normal ? | |
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* Optimize bst_extrapm.m, add waitbar * Use the noise covariance from the database instead of recomputing it |
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* Problem of having inividual trials + averages in the condition => Display warning or not? | |
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* Sources on surface: Display peak regions over time (time = color) => A.Gramfort * Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise) |
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* MRI import: auto-reorientation of MRI after selected NAS / LPA / RPA. * Major bug when importing surfaces for an MRI that was re-oriented manually * Finalize Brodmann scouts * Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND |
* BEM surfaces: * Fix the bumps at the back of the head * Surface edges: same color as the surface when color was changed * Import / registration: * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...) * Auto-reorientation of MRI after selected NAS / LPA / RPA * Major bug when importing surfaces for an MRI that was re-oriented manually * 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 |
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== 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 |
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* Stat on scouts / clusters / "matrix" | |
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== Display == * OpenGL options: {none, software, hardware} * Colormap: Set colormap max with right-click + move on the colorbar * Bug: Mixing 2 views MRI/3d, white cuts appear after !SetCurrentFigure * Bug: Scout without overlay, adapt scale for each graph when "Uniformize" option is unchecked (mixing sources + zscores) * Waitbars: * Replace old waitbars with java ones * Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process) * Contact sheets & movies: use average of time windows instead of single instants, for each picture. == I/O == |
== Input / output == * Use BEM surfaces from !FieldTrip |
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* Stellate * !BrainVision / !BrainAmp: Get functions from EEGLAB |
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* !BrainVision / !BrainAmp: Get functions from EEGLAB | |
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* CTF: * Read continuous RAW files split in several .meg4 files ( > 2 Go) * Read STIM channel and generate !MarkerFile |
* CTF: Read STIM channel and generate !MarkerFile |
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* 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 |
* Output for all the channel file formats |
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== 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 * bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize * 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) |
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* Compile stand-alone version: Linux, MacOS | |
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* 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 |
* 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 |
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* Scouts: Atlases of Tzourio-Mazoyer and Brodman | |
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* 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 | |
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* Display the "What's new" page after downloading new version of brainstorm | |
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== 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 |
== Geeky programming details == * 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 * bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize * Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)... * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way * Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow) * Write shepards.m with new algorithm for nearest neighbors * Use Matlab Coder to compile / optimize some processes * Optimize calls to bst_get, now study and subject have necessarily the same folder name |
What's next
A roadmap to the future developments of Brainstorm.
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
Source modeling
- Computation of equivalent current dipoles
- Display results of CTF SAM beamformer
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
Data management
- Make all the main operations available in the pipeline editor
- Filter the display of the tree by type / name / tag
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:
- Adding events using configurable shortcuts (CTRL+number)
- If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
- Documentation: Add definition of bad segments
- RAW processing:
- Process correctly CTF files saved without the 3rd order grad correction (apply correction before)
- Allow to overwrite RAW files (but with a HUGE warning)
- Update file definition + events if time changes (ex: resample)
- Make it work for 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)
- SSP
- Colormaps:
Define manually minimum => 3 options: [0,max], [-max,max], [min,max]
- Create a colormap similar to MNE, where extrema are bright
- Grey out the portion of the colorbars not displayed because of the threshold
- 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
- Import data:
- Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files)
- Import average only
- Force epochs to be complete (same size for all of them)
- NIRS:
- Add new data type
- Display of sensors by pairs oxy/deoxy (red/blue), overlaid
- 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)
Processes
- Connectivity:
- Circle plot for NxN interactions
- Synthetize + plot N sources into n ROIs (requires scout saved in the surfaces)
- Menu to easily recompute teh sources in ROI form
- Time-frequency:
- Stat computed on time-frequency data
- Validate all the operations on the time-freq files (check for mixed Measures)
- 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 ?)
Complete processing pipeline:
- Do not generate errors, stay silent and generate a report log that is shown at the end
- Import + pre-process
- Sources / head model / noise covariance
- Project sources
- Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions)
- Delete intermediary files
- Complete process of "matrix" file
- Parallel processing: Use parfor
- Distributed processing:
- Version of Brainstorm that can run without JAVA
- Use the BIC/MEG cluster from the pipeline interface (PSOM, P.Bellec)
- SSP:
Display warning if changing the ChannelFlag while there is a Projector applied
- When processing multiple files: waitbar is not behaving well
- Average:
- Remember how many trials were used per channel
- By subject AND condition
- 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 for head movements (using head position coils)
- 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
- Other processes:
- Moving average
- Max
- Median
- Significance test (Dimitrios, Leo)
- Remove linear trend
- Power line removal
- Bug: gradnorm crashes with bad channels
- Spatial smoothing: check / document parameters
- Sinusoid removal: fix new function
Contact sheets & movies: use average of time windows instead of single instants, for each picture.
Database
- Filter display of the database explorer (filename, file type, comment...)
- MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
- GUI: Save configuration of windows (per protocol)
- Add notes in the folders (text files, visible as nodes in the tree)
Source modeling
- Dipole fitting
- Scouts:
- Stocker scouts dans les fichiers de surface
- Downsample scouts with surfaces
- 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 ?
- Define as default
- Check all the processes
- Difference and stat should be: norm(A) - norm(B)
- 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)
- Optimize: grid_interp_mri
- Magnetic extrapolation:
- Do the same thing with EEG
- 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
- Noise covariance matrix:
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)
Anatomy
- BEM surfaces:
- Fix the bumps at the back of the head
- Surface edges: same color as the surface when color was changed
- Import / registration:
- Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...)
- Auto-reorientation of MRI after selected NAS / LPA / RPA
- Major bug when importing surfaces for an MRI that was re-oriented manually
- 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
Statistics
- Stat on scouts / clusters / "matrix"
- 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
Input / output
Use BEM surfaces from FieldTrip
- EEG File formats:
- Stellate
BrainVision / BrainAmp: Get functions from EEGLAB
- Nihon Kohden
- EDF+
EEG CeeGraph
NEUROFILE = COHERENCE EEG/video LongTerm Monitoring => Manfred Spueler
- EGI: Finish support for epoched files (formats 3,5,7)
- 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
Distribution & documentation
- Version with big fonts for live demos
- 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
- 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)
- Processes: Describe all the processes
- Processes: How to write your own processes (user folder for processes)
- Import raw recordings: Add "detect bad trials/channels" in the pipeline
- Temporary folder
- Advanced tutorials:
- EEG (How to import an EEG cap)
How to make and compress a movie (Brainstorm + VirtualDub + XVid)
- Ask users to send their channel files, align on Colin, distribute
Geeky programming details
- 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
- bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
- Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)...
sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way
- Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow)
- Write shepards.m with new algorithm for nearest neighbors
- Use Matlab Coder to compile / optimize some processes
- Optimize calls to bst_get, now study and subject have necessarily the same folder name