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| * 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 ==== * New tools for exploring EEG recordings (custom montages, faster viewer) * Full EEG/epilepsy online tutorial |
* Significance thresholding of the connectivity matrices ==== Documentation ==== * Merging the 12+3 introduction tutorials to illustrate better the latest developments ==== EEG / epilepsy / intra-cranial recordings ==== * Editing the position of intracranial electrodes in the MRI viewer |
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| * 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 |
* Implementation of a new unified minimum norm/beamformer framework |
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| * 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" |
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| * Set the amplidute scale for the time series * CTRL+S : Save modifications |
* 2DLayout: Doesn't work when changing page => need refresh of !GlobalData.Preferences.!TopoLayoutOptions.!TimeWindow * EEG reference/storage: * Intracranial electrodes: Define in the MRI viewer * Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry |
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| * Make it work for all the file formats(at least bandpass filter) | * Make it work for all the file formats (at least bandpass filter + sin removal) |
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| * 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 |
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| * Define manually minimum => 3 options: [0,max], [-max,max], [min,max] | |
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| * 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) |
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| * 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) |
* 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 * Filtering: Use short FIR filters instead of IIR for bandpass, to limit the ringing<<BR>>Or allow the users to edit the !LowStop parameter in bst_bandpass. * Nicer 2D topographies, standardized * Copy figures to clipboard (with the screencapture function) |
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| * Figures: interaction with sensor selection / scouts selections * Display NxN as 1xN * Adapt colormaps for correlation (min and max properties) * PLV: Add a time integration |
* Tutorial coherence [1xN] * Thresholding the connectivity matrices * t-tests on connectivity measures * Graph view: * Fixed scales for intensity sliders * Fix zoom in one region * Text bigger * Too much data in appdata * Other metrics: * Coherence by bands: bst_coherence_band_welch.m * Granger by bands: bst_granger_band.m * Inter-trial coherence |
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| * Circle plot: * Display Neuromag sensors * Event-related coherence? |
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| * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal | |
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| * Scouts values for timefreq on surfaces | |
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| * 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) |
* 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 (Beth) * 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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| * When processing multiple files: waitbar is not behaving well | * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2) |
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| * Apply to continuous recordings for correcting for head movements (using head position coils) | * Apply to continuous recordings for correcting head movements |
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| * Other processes: | * Other processes:<<BR>> |
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| * Optical flow * Simulation: * Fix units in simulation processes => no *1e-9 in "simulate recordings" * Use "add noise" process from Hui-Ling (in Work/Dev/Divers) |
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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 * Rename multiple files == 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/ |
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| * Finish dipole scanning (allow the tab to control multiple figures separately) | |
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| * Scouts: * Represent border as the middle of the adjacent triangles (to have a full segmentation) * Visualize Beamformer results (contact Zainab Fatima): |
* 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 * Visualize Beamformer results: |
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| * Create new file type in the database | |
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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 * 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 |
* Magnetic extrapolation: Do the same thing with EEG |
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| * Display with figure_image() | |
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| * 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? * Processes compute head model and sources: Additional option to set the file comment |
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| * Use the !FreeSurfer subject co-registration (downsample: keep the correspondance) | * 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 * 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 * Clustering cortex: Dimitrios, David, Yu-Teng |
* Use mid-gray instead of pial surface? |
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| * http://www.adscience.fr/uploads/ckfiles/files/html_files/StatEL/statel_wilcoxon.htm * http://www.mathworks.fr/fr/help/stats/signrank.html * Less powerful than t-tests |
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| * t-test on volume sources * Paired t-test on unconstrained sources: (convert to flat + Z-score) => !AnneSo * Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test * http://fr.wikipedia.org/wiki/Test_de_Shapiro-Wilk * http://stats.stackexchange.com/questions/362/what-is-the-difference-between-the-shapiro-wilk-test-of-normality-and-the-kolmog * http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html * http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html * http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab * Create icons for Stat/PAC, Stat/Sprectrum, etc. * One sample t-test across subjects |
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| * MRI: MINC format | * Finish MINC/CIVET integration (finir lecture MINC2: P Bellec) * Send email to CIVET mailing list when done * !FieldTrip structures: In / Out (see fieldtrip/utilities/ft_datatype_*) |
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| * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring | |
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| * !FieldTrip structures: In / Out | |
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| * !FreeSurfer: orig.mgz | * EEGLAB import: Selection of conditions in script mode |
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| * 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 |
* Make the automatic update work when behind a proxy * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * Publication list: Fold by years * Finish existing tutorials: * Dipoles * FieldTrip/Auditory: Extend to MNE/EEGLAB/SPM * New tutorials: * MEG connectome * Describe all the processes * Statistics * Coherence (cortico-muscular ?) * Intra-cranial recordings (Average ref by groups using Comment field) * Co-register MEG runs (Beth) * Missing in the introduction tutorials: * Volume scouts |
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| * First steps: Temporary folder * Exploration: Clusters |
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| * 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 * How to make and compress a movie (Brainstorm + !VirtualDub + XVid) * Ask users to send their channel files, align on Colin, distribute |
* Sources: Model evaluation (by simulating recordings) * Sources: Theshold min. size (not documented yet) * Time-frequency: Description of "log freq scale" option * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm" * Missing in page "Cite Brainstorm": Add all the methods used in the software * Rewrite basic 12+3 tutorials: group in one series == Current bugs == * Black buttons in the MRI Viewer (MacOS) * Workshops: * Create scouts doesn't work: scout created on the other side of the brain * Import anatomy folder: Out of memory sometimes (restart Matlab) * Record tab: Text of epoch number is too big on MacOS * 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 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) * Edit scout in MRI: small modifications cause huge increase of the scout size |
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| * Cleaning surfaces: should work with atlases | |
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| * Zip files created cannot be open with !WinZip * Waitbars: * Replace old waitbars with java ones * 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 |
* Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (Matlab 2014b) |
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| * Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)... | |
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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) * Fix all the 'todo' blocks in the code * Replace handle "0" with bst_get('groot') * At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame) * Error message: Add a link to report directly the bug on the forum |
What's next
A roadmap to the future developments of Brainstorm.
Current topics
Functionnal connectivity
- Significance thresholding of the connectivity matrices
Documentation
- Merging the 12+3 introduction tutorials to illustrate better the latest developments
EEG / epilepsy / intra-cranial recordings
- Editing the position of intracranial electrodes in the MRI viewer
Source modeling
- Implementation of a new unified minimum norm/beamformer framework
Recordings
- RAW file viewer:
- Pre-load next page of recordings
- Documentation: Add definition of bad segments
2DLayout: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
- EEG reference/storage:
- Intracranial electrodes: Define in the MRI viewer
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
- 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
Filtering: Use short FIR filters instead of IIR for bandpass, to limit the ringing
Or allow the users to edit the LowStop parameter in bst_bandpass.- Nicer 2D topographies, standardized
- Copy figures to clipboard (with the screencapture function)
Connectivity
- Tutorial coherence [1xN]
- Thresholding the connectivity matrices
- t-tests on connectivity measures
- Graph view:
- Fixed scales for intensity sliders
- Fix zoom in one region
- Text bigger
- Too much data in appdata
- Other metrics:
- Coherence by bands: bst_coherence_band_welch.m
- Granger by bands: bst_granger_band.m
- Inter-trial coherence
- Work on progress bars
Processes
- Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
- Time-frequency:
- Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
- 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 ?)
- 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 (Beth)
- 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
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.htmlOther 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.
- Optical flow
- Simulation:
Fix units in simulation processes => no *1e-9 in "simulate recordings"
- Use "add noise" process from Hui-Ling (in Work/Dev/Divers)
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
- Rename multiple files
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
Source modeling
- Finish dipole scanning (allow the tab to control multiple figures separately)
- Dipole fitting
- 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
- Visualize Beamformer results:
- Read CTF SAM .svl
- 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:
- 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
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?
- Processes compute head model and sources: Additional option to set the file comment
Anatomy
- 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
- 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
Paired t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo
- Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test
http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html
http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html
http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab
- Create icons for Stat/PAC, Stat/Sprectrum, etc.
- One sample t-test across subjects
Input / output
- Finish MINC/CIVET integration (finir lecture MINC2: P Bellec)
- Send email to CIVET mailing list when done
FieldTrip structures: In / Out (see fieldtrip/utilities/ft_datatype_*)
- EEG File formats:
EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
- BCI2000 Input (via EEGLAB plugin)
- EEGLAB import: Selection of conditions in script mode
Distribution & documentation
- Make the automatic update work when behind a proxy
Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
- Publication list: Fold by years
- Finish existing tutorials:
- Dipoles
- FieldTrip/Auditory: Extend to MNE/EEGLAB/SPM
- New tutorials:
- MEG connectome
- Describe all the processes
- Statistics
- Coherence (cortico-muscular ?)
- Intra-cranial recordings (Average ref by groups using Comment field)
- Co-register MEG runs (Beth)
- Missing in the introduction tutorials:
- Volume scouts
- First steps: Brainstorm preferences
- First steps: Temporary folder
- Exploration: Clusters
- Headmodel: explain the fields + how to get the constrained leadfield
- Sources: Model evaluation (by simulating recordings)
- Sources: Theshold min. size (not documented yet)
- Time-frequency: Description of "log freq scale" option
- Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
- Missing in page "Cite Brainstorm": Add all the methods used in the software
- Rewrite basic 12+3 tutorials: group in one series
Current bugs
- Black buttons in the MRI Viewer (MacOS)
- Workshops:
- Create scouts doesn't work: scout created on the other side of the brain
- Import anatomy folder: Out of memory sometimes (restart Matlab)
- Record tab: Text of epoch number is too big on MacOS
- 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 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)
- Edit scout in MRI: small modifications cause huge increase of the scout size
Geeky programming details
- Hide Java panels instead of deleting them
- mri2scs: convert arguments to meters
- Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (Matlab 2014b)
- 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)
- Fix all the 'todo' blocks in the code
- Replace handle "0" with bst_get('groot')
- At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame)
- Error message: Add a link to report directly the bug on the forum