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| A roadmap for the future developments of Brainstorm. == Next six months == ==== Data acquisition ==== * Improve the acquisition of the head points and the registration MEG / MRI ==== Pre-processing ==== * Extend processing of continuous CTF files to all file formats * Continuous viewer: Many small improvements to the usability of its interface * Improve detection and correction of artifacts with SSP * Co-registration of several MEG runs on one single head position * Make all the main operations available in the pipeline editor ==== File formats ==== * MRI: MINC * EEG: Stellate * EEG: Brain Products / !BrainAmp * Read and display NIRS recordings * CTF SAM Beamformer results |
A roadmap to the future developments of Brainstorm. == Current topics == |
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| * Implementation of methods developed at USC <<BR>><<BR>> == Full to-do list == ==== Recordings ==== |
* 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 ==== * New tools for exploring EEG recordings (custom montages, faster viewer) * 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 <<BR>><<BR>><<BR>> == Recordings == |
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| * Buttons for changing scales (time + amplitude) * Add tooltips to all the buttons / shortcuts * Adding events using configurable shortcuts (CTRL+number) |
* Pre-load next page of recordings * Allow multiple RAW windows(columns display) * Screen setups * Time scale: define in fixed s/mm (like the CTF tools) * Secondary windows: display length of time selection |
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| * Set the amplidute scale for the time series * CTRL+S : Save modifications |
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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 the file formats * Homogenize a selection of several subjects/conditions * Popup menu when more than one study selected * Creation of a common channel file (match channels by names, not by order) * Register MEG runs (recompute fields for a different set of sensors, MEGCoregister from old brainstorm) |
* Make it work for all the file formats(at least bandpass filter) * Events: advanced process for recombining. Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html * Improve interface for SSP on imported recordings * Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry * 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 ==== Pre-processing ==== |
* 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 * Intracranial electrodes: * Define and display in the MRI viewer * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab) == Connectivity == * Figures: interaction with sensor selection / scouts selections * Display NxN as 1xN * Adapt colormaps for correlation (min and max properties) * PLV: Add a time integration * Work on progress bars * Circle plot: * Display Neuromag sensors * Event-related coherence? == Processes == * SImulation: Input as a text with a syntax "scoutname = f1(t) + white_noise(t) + ..." * 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 ?) * Distributed processing: * Version of Brainstorm that can run without JAVA |
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| * Make SSP projections dynamic, and keep the full list instead of always them combining them * Take the bad channels in account in the application of the SSP * Refresh display after changing the list of bad channels (imported files + raw) so the SSP are applied correctly * When processing multiple files: waitbar is all messed up * Tune parameters for the automatic detection of heartbeats and eye blinks * Write documentation * Complete processing pipeline: * Import + pre-process * Sources / head model / noise covariance * Project sources * Do not generate errors, stay silent and generate a report log that is shown at the end |
* 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 * 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) * Current Source Density (CSD) => Ghislaine<<BR>>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html * Other processes: * Moving average * Max * Median * Significance test (Dimitrios, Leo) * Spatial smoothing: check / document parameters * Contact sheets & movies: use average of time windows instead of single instants, for each picture. == 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: * Represent border as the middle of the adjacent triangles (to have a full segmentation) |
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| * == Other new features == * Intracranial electrodes: * Display in the MRI viewer * Different data type * Display time series * Stat on scouts / clusters / "matrix" * Average: * Remember how many trials were used per channel * By subject AND condition * Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions) * GUI: Save configuration of windows (per protocol) * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions. * Sources on surface: Display peak regions over time (time = color) => A.Gramfort * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab) * Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise) * Add notes in the folders (text files, visible as nodes in the tree) * Contact sheets & movies: use average of time windows instead of single instants, for each picture. == Source modeling == |
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| * 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 |
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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) * 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) * Calculate !ImagingKernel * Gain for a scout |
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| * * BEM: * Fix the bumps at the back of the head * Surface edges: same color as the surface when color was changed * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...) * Use BrainVISA / !FreeSurfer labeling automatically when importing cortex surface * ICBM brain * MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab * ICBM average surfaces + atlas * Using CIVET pipeline for extracting surfaces s * MRI import: auto-reorientation of MRI after selected NAS / LPA / RPA. * Major bug when importing surfaces for an MRI that was re-oriented manually * Finalize Brodmann scouts * Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND * Clustering cortex: Dimitrios, David, Yu-Teng == Processes == * Other processes: * Moving average * Remove linear trend * Power line removal * Bug: gradnorm crashes with bad channels * Spatial smoothing: check / document parameters * Sinusoid removal: fix new function * Time-frequency: * Write script for timefreq tutorial * Make much faster and more memory efficient (C functions coded by Matti ?) * Power spectrum: computation (FFT/welch, or average of TF) + display(f/Power, 2DLayout) * Display stat computed on time-frequency data * Display TF maps separately for the two gradiometers (if not: overlap) * Source reconstruction by frequency bands * Scouts on surface / time-freq * Process selection interface: * Do not reload the list a each display, but once when starting Brainstorm * Popup menus: Add a "Process" menu with all the available processes * Bug when redimensioning window (with more than one process) * isAvgRef: warning quand process necessite des donnees en AVG REF en entree * Save "freqband" option when edited from custom processes |
* Scouts: * Mix constrained/unconstrained/volume sources, using the Structures 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 * Generate mixed density surfaces * Import / registration: * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...) * Use Metch (iso2mesh) * Major bug when importing surfaces for an MRI that was re-oriented manually * Use mid-gray instead of pial surface? |
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| == Display == == I/O == |
== Input / output == |
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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 | * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring |
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| * Other file formats * MEG160 (KIT) * CTF: Read STIM channel and generate !MarkerFile * EEGLAB: Apply ICA matrices, get number of trials for AVG files * !FieldTrip structures: In / Out * Gzipped Nifti (new BrainVISA standard) * Output for all the channel file formats * Analyze / Nifti:<<BR>> * Fix output function (output MRIs cannot be imported in SPM) * Use correctly field "orient" to align automatically MRI when importing * Define scouts from SPM / Analyze 3D masks * Files > 2Gb: display warnings |
* !FieldTrip structures: In / Out * BCI2000 Input (via EEGLAB plugin) == Distribution & documentation == * 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 * First steps: Brainstorm preferences * Headmodel: explain the fields + how to get the constrained leadfield * 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 * How to export sources for analysis in SPM * Advanced tutorials: * EEG (How to import an EEG cap) * Epilepsy / spike analysis * Ask users to send their channel files, align on Colin, distribute |
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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 |
* Matlab/Java memory leaks * Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal * Hide Java panels instead of deleting them * mri2scs: convert arguments to meters * Waitbars: Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process) |
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| * Bug node selection: click on sources > TF: select node-source, not node-condition | |
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| * 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 |
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== Distribution & documentation == * Version with big fonts for live demos * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * List of all the shortcuts * Send email to registered users to anounce major improvements * Script tutorials: * Update them to reflect all the recent changes * Script for the time-frequency computation * Introduction tutorials: * Estimate time to complete each tutorial * Clusters * Anatomy: Segmentation with !FreeSurfer * First steps: Brainstorm preferences * Headmodel: explain the fields + how to get the constrained leadfield * Coordinate sytems: How to convert between the different coordinates systems in scripts * Sources: Modelized data * Sources: theshold min. size (not documented yet) * Scouts: Atlases of Tzourio-Mazoyer and Brodman * Processes: Describe all the processes * Processes: How to write your own processes (user folder for processes) * Processes: Processing RAW files * Import raw recordings: Add "detect bad trials/channels" in the pipeline * Advanced tutorials: * MNE sample dataset * EEG (How to import an EEG cap) * MRI segmentation with !FreeSurfer => David Wheland * How to make and compress a movie (Brainstorm + !VirtualDub + XVid) * Display the "What's new" page after downloading new version of brainstorm * Ask users to send their channel files, align on Colin, distribute |
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
- New tools for exploring EEG recordings (custom montages, faster viewer)
- 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
- 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 amplidute scale for the time series
- CTRL+S : Save modifications
- RAW processing:
- Make it work for all the file formats(at least bandpass filter)
Events: advanced process for recombining. Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
- Improve interface for SSP on imported recordings
Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry
- 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)
- 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
- Intracranial electrodes:
- Define and display in the MRI viewer
- Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)
Connectivity
- Figures: interaction with sensor selection / scouts selections
- Display NxN as 1xN
- Adapt colormaps for correlation (min and max properties)
- PLV: Add a time integration
- Work on progress bars
- Circle plot:
- Display Neuromag sensors
- Event-related coherence?
Processes
- SImulation: Input as a text with a syntax "scoutname = f1(t) + white_noise(t) + ..."
- 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 ?)
- Distributed processing:
- Version of 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
- 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 for head movements (using head position coils)
Current Source Density (CSD) => Ghislaine
http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html- Other processes:
- Moving average
- Max
- Median
- Significance test (Dimitrios, Leo)
- Spatial smoothing: check / document parameters
Contact sheets & movies: use average of time windows instead of single instants, for each picture.
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:
- Represent border as the middle of the adjacent triangles (to have a full segmentation)
- 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
- 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
Anatomy
- Scouts:
- Mix constrained/unconstrained/volume sources, using the Structures 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
- Generate mixed density surfaces
- Import / registration:
- Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...)
- Use Metch (iso2mesh)
- 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
Input / output
- EEG File formats:
EEG CeeGraph
NEUROFILE = COHERENCE EEG/video LongTerm Monitoring
- EGI: Finish support for epoched files (formats 3,5,7)
FieldTrip structures: In / Out
- BCI2000 Input (via EEGLAB plugin)
Distribution & documentation
- 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
- First steps: Brainstorm preferences
- Headmodel: explain the fields + how to get the constrained leadfield
- 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
- How to export sources for analysis in SPM
- Advanced tutorials:
- EEG (How to import an EEG cap)
- Epilepsy / spike analysis
- Ask users to send their channel files, align on Colin, distribute
Geeky programming details
- Matlab/Java memory leaks
- Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal
- Hide Java panels instead of deleting them
- mri2scs: convert arguments to meters
- Waitbars: Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process)
- Bug: Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)
- 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)...
- Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow)
- Optimize calls to bst_get, now study and subject have necessarily the same folder name