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| ==== 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 ==== * 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 |
==== Documentation ==== * New online tutorials (work in progress) |
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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 <<BR>><<BR>><<BR>> |
* Implementation of a new unified minimum norm/beamformer framework (work in progress) ==== Functional connectivity ==== * Significance thresholding of the connectivity matrices (2016) ==== Computation ==== * Removing the dependence to the Java interface to run in headless mode (not started) * Interacting directly with distributed computing systems (not started) <<BR>><<BR>> |
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| * Nicer 2D topographies, standardized (using FieldTrip .lay files?) * 2DLayout: * Use the same standard positions, too much space between sensors (Recordings + TF) * Overlay multiple conditions * RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow * Same shortcuts as the raw file viewer (right-click + move for gain) |
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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" * 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 |
* Events: advanced process for recombining. * Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html * Bad channels specified at the program level (for sites that have permanent bad channels: AS) * 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 * 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. * Show easily recordings maximum/values in the file viewer * SEEG/ECOG: Display SEEG+ECOG contacts at the same time == Interface == |
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| * Define manually minimum => 3 options: [0,max], [-max,max], [min,max] | * Manage multiple custom colormaps * Allow brightness/contrast manipulations on the custom colormaps |
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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) * 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) |
* Global colormap max: Should get the maximum across all the open files * Open new figures as tab (docked in the Figures window) * Copy figures to clipboard (with the screencapture function) * Removing all the CTRL and SHIFT in the keyboard shortcuts * Display warning before opening files that are too big |
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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 * Work on progress bars * Circle plot: * Display Neuromag sensors * Event-related coherence? |
* Thresholding the connectivity matrices * t-tests on connectivity measures * Check why our Hilbert implementation has huge edge effects * Connectivity based on band limited power (Sylvain): * Compute Hilbert/Bandpass + correlation of the envelopes * Bandpass envelopes before computing correlations? * Compute Hilbert(sensors) and then project to source space? * Multi-tapers? * Graph view: * Re-write using pure Matlab code and smoothed graphics * Fixed scales for intensity sliders * Text bigger * Too much data in appdata * Fixed scales for intensity sliders * Add "=" shortcut for having graphs with similar configurations * Disable zoom in one region (serious bugs) * Coherence: * Average cross-spectra instead of concatenating epochs (to avoid discontinuities) * Granger: * Crashes sometimes: improve stability * Re-write and optimize code * Add progress bar * PLV: * Add p-values * Remove evoked * Optimize code * Add time integration * Unconstrained sources * PAC: * Refine frequency vector of low frequencies * How many central frequencies to use in bst_pac? * Change filters: no chirplet functions * bst_freqfilter: Use nfcomponents like in bst_pac * Esther recommended a larger frequency binning of the PAC estimation * Other metrics: * Coherence by bands: bst_coherence_band_welch.m * Granger by bands: bst_granger_band.m * Inter-trial coherence * Tutorial coherence [1xN] : Reproduce FieldTrip results? |
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| * SImulation: Input as a text with a syntax "scoutname = f1(t) + white_noise(t) + ..." | * ICA: * Exploration: Add window with spectral decomposition (useful for muscle artifacts) * Comparison JADE/Infomax: <<BR>> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135 * Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig) * Dimension reduction with PCA adds artifacts: Not done by default in EEGLAB<<BR>>Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )<<BR>>Student Carl Leichter detailed this in his thesis * S Makeig: Use ICA to select the IC of interest instead of only removing artifacts * Display of spectrum for components (PSD/FFT) * Distributed processing: Brainstorm that can run without Java * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal * Allow processes in Python and Java * Optimize opening time for the menu "Add process" * SSP: * Display warning if changing the ChannelFlag while there is a Projector applied * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2) * Bandpass: * Offer option: bst_bandpass_fft / bst_bandpass_filter * Rewrite without the forced low-pass filter at Fs/3 * Show warning when using inappropriate high-pass filter (precision too high) * Use FIR filter * Spectral flattening (John): * ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis * PSD: * Rewrite to have the same input as coherence * Normalize with the total power (TF/sum(TF,3)) * Remove line noise: http://www.nitrc.org/projects/cleanline * Band-limited power envelope * Reports: * Save as HTML / PDF * Do not display the intermediate files * Pipeline editor: * Add loops over subjects/conditions/trial groups |
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| * Standardize using: diff before calculation + cumsum (checkbox "flatten data") | |
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| * Scouts values for timefreq on surfaces * How to combine 3 orientations for unconstrained sources |
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| * 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 |
* TF scouts: should display average of TF maps * Impossible to keep complex values for unconstrained sources * Pad short epochs with zero values for getting lower frequencies * Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead. * 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 * Allow the detection on differences of signals (bipolar montages) |
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| * 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 |
* Apply to continuous recordings for correcting head movements * Resample continuous files |
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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...) | * Optimize startup speed * Start Brainstorm without Java (-nodesktop) * Sort files by 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 * Allow matrix files to be attached to other 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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| * Dipole fitting * Scouts: * Represent border as the middle of the adjacent triangles (to have a full segmentation) * Visualize Beamformer results (contact Zainab Fatima): |
* Dipoles: * Finish dipole scanning (allow the tab to control multiple figures separately) * Dipole fitting: We will not implement non-linear fits, recommended use of dense volume grids * panel_dipoles: Doesn't work with multiple figures * Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates * Panel Get coordinates: Add button "find maximum" * Create scout form maximum: Not available yet for mixed/volume head model. * Stenroos 2014 paper: Include the following methods * Inner and outer skull surfaces generator from FieldTrip (needs SPM) * Nolte corrected-sphere model (good model re:Alex) * Fast BEM models * Visualize Beamformer results: |
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| * Create new file type in the database | |
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| * Compute unconstrained and then project on the normal ? * Define as default * Check all the processes * Difference and stat should be: norm(A) - norm(B) |
* Stat and connectivity: what to do? (re-send email John+Sylvain) |
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| * Scouts 3D | |
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| * Optimize: 3D display (better that 9x9 cubes) | * Optimize: 3D display (better than 9x9 cubes) |
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| * Optimize: grid_interp_mri * Magnetic extrapolation: * Do the same thing with EEG |
* Magnetic extrapolation: Do the same thing with EEG |
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| * Display with figure_image() | |
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| * When deploying to other conditions: Apply destination SSP (!NoiseCov = SSP . !NoiseCov . SSP' ) | * When deploying to other conditions: Apply destination SSP (NoiseCov = SSP . NoiseCov . SSP' ) |
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| * Calculate !ImagingKernel * Gain for a scout | * 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 * Time-frequency beamformers: * Band-pass everything in different frequency bands + Source estimation + TF * Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF * Display volume scouts and surface scouts at the same time * Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm) * BEM: Fix unstable results when one vertex is too close from the layers (5mm ?) * Hui-Ling beamformers: * More explanations about what is in NAI and Spatial filters * Explain that is this is better to study effects extended in time (Ntime > Nsensors) * Group LCMV+MCB * Condition LEFT median nerve: very bad results * Menu Sources > Simulate recordings: * Do not close the 3D figures after generating a new file * Add a process equivalent to this menu |
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| * Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned * Project all sub-cortical structures to default anatomy * Warping: Scale option has to be fixed, it is currently very unstable |
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| * Mix constrained/unconstrained/volume sources, using the "Source model" atlas | |
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| * Project scouts betweens subjects and between hemispheres | |
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| * Sort scouts by region in process options * Co-register MRI and CT for electrodes marking in the MRI Viewer |
|
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| * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...) * Use Metch (iso2mesh) |
|
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| * Smooth surface: Fix little spikes to irregularities in the mesh * Menu head model > Copy to other conditions/subjects (check if applicable first) * Add cerebellum to default model generated with "Import FS anatomy" * Add eyes models to attract eye activity |
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| * ANOVA: Use LENA functions | * ANOVA: Use LENA functions(?) |
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| * 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 * http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock * http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq * Threshold in time: keep only the regions that are significative for contiguous blocks of time, or over a certain number of time points<<BR>> => Process that creates a static representation of a temporal window |
* Problem t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo * Waiting for test from Dimitrios * 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 * Stat FieldTrip: impossible to do Abs(Mean(Sources)) => Is it a problem? * PLS: Partial Least Squares |
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| * FieldTrip structures: Import/Export continuous recordings and non-averaged trials. | |
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| * EEG !CeeGraph * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring |
* EEG CeeGraph |
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| * !FieldTrip structures: In / Out | |
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| * EEGLAB import: * Support for binary AND epoched files (now it's one or the other) * Allow epoched files with recordings saved in external files (now external files implies continuous recordings) * BST-BIN: Add compression * Review raw on all the file formats (ASCII EEG and Cartool missing) * gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports. |
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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 * 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 |
* Reference tutorials on Google scholar + ResearchGate * Cleaning threads on the forum * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * Finish existing tutorials: * Dipoles * Auditory: Finish scripts * Group MEM/Epilepsy + Epilepsy tutorials * New tutorials: * MEG connectome * Scrambled faces (SPM/MNE-Python) * Coherence (cortico-muscular ?) * Intra-cranial recordings * Co-register MEG runs (Beth) * Missing in the introduction tutorials: * Volume scouts * Sources: Model evaluation (by simulating recordings) * Time-frequency: Description of "log freq scale" option * Modify a structure manually: Export to Matlab/Import from Matlab * File manipulation: file_short, file_fullpath, in_bst_*... * Description of all fields in MRI and surfaces * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm" * Missing in page "Cite Brainstorm": Add all the methods used in the software == Current bugs == * Interface looks small on screens with very high resolutions: Reduce the resolution * Workshops: * Import anatomy folder: Out of memory on Win 32bits (restart Matlab) * Compute head model: Out of memory on Win 32bits * Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz) * Cannot import two .ds folders at once * Colors inverted in the PSD/TF plots (power vs. log) * Cannot type the name of a channel in "Detect ECG" * Image viewer: Difficult to get to 100% * Canolty maps computation: Fix progress bar * Smooth TF windows that contain multiple plots * 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 * Edit scout in MRI: small modifications cause huge increase of the scout size * Reports: Text size is too small with Java 1.5 (2006b-2007a) * Optimize MRI viewer with patch() instead of image() * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call * 2DLayout (time series): * Sometimes the lines are not visible * Does not work when DC offset is not removed * 2DLayout (TF): Images are too far apart with EEG 20 channels * Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10 * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG. |
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| * Matlab/Java memory leaks * Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal |
|
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| * 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 |
* Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b) |
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| * 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 |
* Shared kernels: "get bad channels" operation in a different way (reading all the files is too slow) * Optimize bst_get: * Now study and subject have necessarily the same folder name * Replace big switch with separate functions * Progress bar: * Add different levels (to handle sub-processes) * Make work correctly with RAW on resting tutorial * Uniformize calls in bst_process/Run * Add a "Cancel" button * Fix all the 'todo' blocks in the code * 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 * in_bst_results (isFull=1): DataFile should be relative |
What's next
A roadmap to the future developments of Brainstorm.
Current topics
Documentation
- New online tutorials (work in progress)
Source modeling
- Implementation of a new unified minimum norm/beamformer framework (work in progress)
Functional connectivity
- Significance thresholding of the connectivity matrices (2016)
Computation
- Removing the dependence to the Java interface to run in headless mode (not started)
- Interacting directly with distributed computing systems (not started)
Recordings
Nicer 2D topographies, standardized (using FieldTrip .lay files?)
- 2DLayout:
- Use the same standard positions, too much space between sensors (Recordings + TF)
- Overlay multiple conditions
RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
- Same shortcuts as the raw file viewer (right-click + move for gain)
- RAW file viewer:
- Pre-load next page of recordings
- Events: advanced process for recombining.
Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
- Bad channels specified at the program level (for sites that have permanent bad channels: AS)
- 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
- 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.
- Show easily recordings maximum/values in the file viewer
- SEEG/ECOG: Display SEEG+ECOG contacts at the same time
Interface
- Colormaps:
- Manage multiple custom colormaps
- Allow brightness/contrast manipulations on the custom colormaps
- Create a colormap similar to MNE, where extrema are bright
- Global colormap max: Should get the maximum across all the open files
- Open new figures as tab (docked in the Figures window)
- Copy figures to clipboard (with the screencapture function)
- Removing all the CTRL and SHIFT in the keyboard shortcuts
- Display warning before opening files that are too big
Connectivity
- Thresholding the connectivity matrices
- t-tests on connectivity measures
- Check why our Hilbert implementation has huge edge effects
- Connectivity based on band limited power (Sylvain):
- Compute Hilbert/Bandpass + correlation of the envelopes
- Bandpass envelopes before computing correlations?
- Compute Hilbert(sensors) and then project to source space?
- Multi-tapers?
- Graph view:
- Re-write using pure Matlab code and smoothed graphics
- Fixed scales for intensity sliders
- Text bigger
- Too much data in appdata
- Fixed scales for intensity sliders
- Add "=" shortcut for having graphs with similar configurations
- Disable zoom in one region (serious bugs)
- Coherence:
- Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
- Granger:
- Crashes sometimes: improve stability
- Re-write and optimize code
- Add progress bar
- PLV:
- Add p-values
- Remove evoked
- Optimize code
- Add time integration
- Unconstrained sources
- PAC:
- Refine frequency vector of low frequencies
- How many central frequencies to use in bst_pac?
- Change filters: no chirplet functions
- bst_freqfilter: Use nfcomponents like in bst_pac
- Esther recommended a larger frequency binning of the PAC estimation
- Other metrics:
- Coherence by bands: bst_coherence_band_welch.m
- Granger by bands: bst_granger_band.m
- Inter-trial coherence
Tutorial coherence [1xN] : Reproduce FieldTrip results?
Processes
- ICA:
- Exploration: Add window with spectral decomposition (useful for muscle artifacts)
Comparison JADE/Infomax:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135- Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)
Dimension reduction with PCA adds artifacts: Not done by default in EEGLAB
Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )
Student Carl Leichter detailed this in his thesis- S Makeig: Use ICA to select the IC of interest instead of only removing artifacts
- Display of spectrum for components (PSD/FFT)
- Distributed processing: Brainstorm that can run without Java
- Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
- Allow processes in Python and Java
- Optimize opening time for the menu "Add process"
- 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)
- Bandpass:
- Offer option: bst_bandpass_fft / bst_bandpass_filter
- Rewrite without the forced low-pass filter at Fs/3
- Show warning when using inappropriate high-pass filter (precision too high)
- Use FIR filter
- Spectral flattening (John):
- ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis
- PSD:
- Rewrite to have the same input as coherence
- Normalize with the total power (TF/sum(TF,3))
Remove line noise: http://www.nitrc.org/projects/cleanline
- Band-limited power envelope
- Reports:
- Save as HTML / PDF
- Do not display the intermediate files
- Pipeline editor:
- Add loops over subjects/conditions/trial groups
- Time-frequency:
- Standardize using: diff before calculation + cumsum (checkbox "flatten data")
- Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
- 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
- Impossible to keep complex values for unconstrained sources
- Pad short epochs with zero values for getting lower frequencies
- Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead.
- 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
- Allow the detection on differences of signals (bipolar montages)
- 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
- Resample continuous files
- 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.
- 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
- Optimize startup speed
- Start Brainstorm without Java (-nodesktop)
- Sort files by comment
- 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
- Allow matrix files to be attached to other 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
- Dipoles:
- Finish dipole scanning (allow the tab to control multiple figures separately)
- Dipole fitting: We will not implement non-linear fits, recommended use of dense volume grids
- panel_dipoles: Doesn't work with multiple figures
- Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates
- Panel Get coordinates: Add button "find maximum"
- Create scout form maximum: Not available yet for mixed/volume head model.
- Stenroos 2014 paper: Include the following methods
Inner and outer skull surfaces generator from FieldTrip (needs SPM)
- Nolte corrected-sphere model (good model re:Alex)
- Fast BEM models
- Visualize Beamformer results:
- Read CTF SAM .svl
- Display as layers in the MRI viewer
- Unconstrained sources:
- Stat and connectivity: what to do? (re-send email John+Sylvain)
- Overlapping spheres: improve the estimation of the spheres for the frontal lobes
- Volume grid:
- Test volume sources with all the subsequent processes (timefreq, stat...)
- Optimize: 3D display (better than 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
- Time-frequency beamformers:
- Band-pass everything in different frequency bands + Source estimation + TF
- Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF
- Display volume scouts and surface scouts at the same time
- Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
- BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
- Hui-Ling beamformers:
- More explanations about what is in NAI and Spatial filters
Explain that is this is better to study effects extended in time (Ntime > Nsensors)
- Group LCMV+MCB
- Condition LEFT median nerve: very bad results
Menu Sources > Simulate recordings:
- Do not close the 3D figures after generating a new file
- Add a process equivalent to this menu
Anatomy
Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned
- Project all sub-cortical structures to default 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
- Display scouts in a tree: hemisphere, region, subregion
- Downsample to atlas: allow on timefreq/connect files
- Sort scouts by region in process options
- Co-register MRI and CT for electrodes marking in the MRI Viewer
- 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?
- Smooth surface: Fix little spikes to irregularities in the mesh
Menu head model > Copy to other conditions/subjects (check if applicable first)
- Add cerebellum to default model generated with "Import FS anatomy"
- Add eyes models to attract eye activity
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
Problem t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo
- Waiting for test from Dimitrios
- 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
Stat FieldTrip: impossible to do Abs(Mean(Sources)) => Is it a problem?
- PLS: Partial Least Squares
Input / output
FieldTrip structures: Import/Export continuous recordings and non-averaged trials.
- EEG File formats:
EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
- BCI2000 Input (via EEGLAB plugin)
- EEGLAB import:
- Support for binary AND epoched files (now it's one or the other)
- Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
- BST-BIN: Add compression
- Review raw on all the file formats (ASCII EEG and Cartool missing)
- gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.
Distribution & documentation
Reference tutorials on Google scholar + ResearchGate
- Cleaning threads on the forum
Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
- Finish existing tutorials:
- Dipoles
- Auditory: Finish scripts
- Group MEM/Epilepsy + Epilepsy tutorials
- New tutorials:
- MEG connectome
- Scrambled faces (SPM/MNE-Python)
- Coherence (cortico-muscular ?)
- Intra-cranial recordings
- Co-register MEG runs (Beth)
- Missing in the introduction tutorials:
- Volume scouts
- Sources: Model evaluation (by simulating recordings)
- Time-frequency: Description of "log freq scale" option
- Modify a structure manually: Export to Matlab/Import from Matlab
- File manipulation: file_short, file_fullpath, in_bst_*...
- Description of all fields in MRI and surfaces
- Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
- Missing in page "Cite Brainstorm": Add all the methods used in the software
Current bugs
- Interface looks small on screens with very high resolutions: Reduce the resolution
- Workshops:
- Import anatomy folder: Out of memory on Win 32bits (restart Matlab)
- Compute head model: Out of memory on Win 32bits
- Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz)
- Cannot import two .ds folders at once
- Colors inverted in the PSD/TF plots (power vs. log)
- Cannot type the name of a channel in "Detect ECG"
- Image viewer: Difficult to get to 100%
- Canolty maps computation: Fix progress bar
- Smooth TF windows that contain multiple plots
- 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
- Edit scout in MRI: small modifications cause huge increase of the scout size
- Reports: Text size is too small with Java 1.5 (2006b-2007a)
- Optimize MRI viewer with patch() instead of image()
- Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
- 2DLayout (time series):
- Sometimes the lines are not visible
- Does not work when DC offset is not removed
- 2DLayout (TF): Images are too far apart with EEG 20 channels
- Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
- Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG.
Geeky programming details
- Hide Java panels instead of deleting them
- Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)
- bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
- Shared kernels: "get bad channels" operation in a different way (reading all the files is too slow)
- Optimize bst_get:
- Now study and subject have necessarily the same folder name
- Replace big switch with separate functions
- Progress bar:
- Add different levels (to handle sub-processes)
- Make work correctly with RAW on resting tutorial
- Uniformize calls in bst_process/Run
- Add a "Cancel" button
- Fix all the 'todo' blocks in the code
- 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
in_bst_results (isFull=1): DataFile should be relative