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A to-do list for the development of Brainstorm in the next few years == New interface elements == * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions. * Functionnal connectivity (display: see eConnectome) * SSP: * Make SSP projections dynamic, and keep the full list instead of always them combining them * Take the bad channels in account in the application of the SSP * Refresh display after changing the list of bad channels (imported files + raw) so the SSP are applied correctly |
A roadmap to the future developments of Brainstorm. == Current topics == ==== Data acquisition ==== * Improve the acquisition of the head points and the registration MEG / MRI * Real-time processing and display (based on !FieldTrip realtime module) * Support for intra-cranial recordings ==== Pre-processing ==== * Correction for head movements (using the continuous head localization coils) ==== Source modeling ==== * Computation of equivalent current dipoles * Display results of CTF SAM beamformer ==== Functionnal connectivity ==== * Integration of different metrics to study the brain connectivity: <<BR>>Correlation, coherence, Granger causality, phase locking value * Development of new ways to represent the connectivity between sensors or brain regions ==== Data management ==== * Filter the display of the tree by type / name / tag ==== Large scale analysis ==== * Parallel processing: Reduce the computation times using the parallel processing toolbox * Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters <<BR>><<BR>><<BR>> == Recordings == * RAW file viewer: * Pre-load next page of recordings * Allow multiple RAW windows * 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 cale 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 * Imported recordings: Offer the same interface as the RAW viewer: * Scroll bar * Events viewer / editor * Re-epoch (import from files in database) * SSP * 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 * Sources on surface: Display peak regions over time (time = color) => A.Gramfort * Homogenize a selection of several subjects/conditions * Popup menu when more than one study selected * Creation of a common channel file (match channels by names, not by order) * Register MEG runs (recompute fields for a different set of sensors, MEGCoregister from old brainstorm) |
* 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 |
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* Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise) * Interface to compute reaction times based on events: <<BR>>Input:selection of cue event + event response; Output: reation time trial by trial, average, std, distribution... => Etienne Labyt * Database navigator: F4 to switch to next sourcefile * Segmentation in microstates |
== Connectivity == * Figures: interaction with sensor selection / scouts selections * Calculation and use of p-values for the metrics * Trial analysis: Concatenations rather than averages for most metrics * Optimize bst_coherence * 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 * Use little squares * Little squares with scout color instead of point * Max distance slider: useless * Event-related coherence? == Processes == * Time-frequency: * Stat computed on time-frequency data * Validate all the operations on the time-freq files (check for mixed Measures) * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...) * Scouts values for timefreq on surfaces * How to combine 3 orientations for unconstrained sources * Display logs as negative * 2D Layout in spectrum * Make much faster and more memory efficient (C functions coded by Matti ?) * Parallel processing: Use parfor * Distributed processing: * Version of Brainstorm that can run without JAVA * Use the BIC/MEG cluster from the pipeline interface (PSOM, P.Bellec) * SSP: * Display warning if changing the !ChannelFlag while there is a Projector applied * When processing multiple files: waitbar is not behaving well * Average: * Remember how many trials were used per channel * By subject AND condition * Save standard deviation * Display standard deviation as a halo around the time series * Co-registration of MEG runs: * SSP: Group projectors coming from different files * Finish validation of the method * Apply to continuous recordings for correcting for head movements (using head position coils) * 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) |
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* Inverse: * Stable LCMV Beamformer * MUSIC * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way |
* Dipole fitting * Scouts: * 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 |
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* Compute unconstrained and then project on the normal ? | |
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* Optimize bst_extrapm.m, add waitbar * Use the noise covariance from the database instead of recomputing it |
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* 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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* 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 |
* Use the FreeSurfer subject co-registration (downsample: keep the correspondance) * Import / registration: * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...) * Auto-reorientation of MRI after selected NAS / LPA / RPA * Major bug when importing surfaces for an MRI that was re-oriented manually * ICBM brain * MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab * ICBM average surfaces + atlas * Using CIVET pipeline for extracting surfaces |
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== Processes == * Important new processes for a full processing pipleline: * Import, and segmentation of RAW files * Detect bad segments on RAW (then events in "bad" segments would be ignored) * Artifact detection: use other things than simple value thresholds (like variance of the sensors...) * Create events list based on thresholds on some channels (Stim, EOG, ECG...) => Etienne Labyt * Creation of SSP vectors (ex: Remove cardiac artifac) * ICA * Integration of Antoine Ducorps methods (everything in the doc of the dataHandler): * Cardiac artifact correction in MEG * PCA correction of ocular artifacts * Interpolation of missing EEG canal * Headmodel / sources / noise cov * Project sources * Delete intermediary files * Processing raw/continuous: * Process non-FIF files (need to convert the header) * Apply SSP + CTF Compensators(only if it useful - maybe create a specific process for that) * Other processes: * Bug: gradnorm crashes with bad channels * Spatial smoothing: check / document parameters * Sinusoid removal: fix new function * Time-frequency: * Write script for timefreq tutorial * Make much faster and more memory efficient (C functions coded by Matti ?) * Power spectrum: computation (FFT/welch, or average of TF) + display(f/Power, 2DLayout) * Display stat computed on time-frequency data * Display TF maps separately for the two gradiometers (if not: overlap) * Source reconstruction by frequency bands * Scouts on surface / time-freq * Process selection interface: * Bug when redimensioning window (with more than one process) * isAvgRef: warning quand process necessite des donnees en AVG REF en entree * Save "freqband" option when edited from custom processes * John's noise cancellation filters * Chain calls of similar processes (ex. bandpass+sin_remove), to avoid reading the full raw files several times |
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* Stat on scouts / clusters / "matrix" | |
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== Display == * OpenGL options: {none, software, hardware} * Colormap: Set colormap max with right-click + move on the colorbar * Bug: Mixing 2 views MRI/3d, white cuts appear after !SetCurrentFigure * Bug: Scout without overlay, adapt scale for each graph when "Uniformize" option is unchecked (mixing sources + zscores) * Waitbars: * Replace old waitbars with java ones * Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process) * Contact sheets & movies: use average of time windows instead of single instants, for each picture. == I/O == |
== Input / output == * MRI: MINC format |
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* Nihon Kohden * EDF+ * !BrainVision / !BrainAmp: Get functions from EEGLAB |
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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 continuous RAW files split in several .meg4 files ( > 2 Go) * 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) * Analyze / Nifti:<<BR>> * Fix output function (output MRIs cannot be imported in SPM) * Use correctly field "orient" to align automatically MRI when importing |
* !FieldTrip structures: In / Out * BCI2000 Input (via EEGLAB plugin) |
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* Files > 2Gb: display warnings == Programming details == * Double-click doesn't work well on some Linux workstations * Bug: Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects) * Bug node selection: click on sources > TF: select node-source, not node-condition * Bug tree_dependencies: sources files, reprojected on default anatomy; If based on data files that are bad trials, they should be ignored by tree_dependencies, and they are not * bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize * Testing functions: test_ctf "folder" / test_neuromag "folder" / test "folder" => Alex * Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)... * Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow) * Rewrite all GUI functions with gui_component * Remove field "!BrainStormSubject" in the studies file: force same folder name for anat & data * Allow protocols with same folder for anat and data * Ensure that all the loaded and saved filenames are in "unix" format * Use parfor: When not available, replace directly all the "parfor" with "for" in file.m * Use Matlab GPU toolbox * Re-use panels instead of delete+create again * Optimize bst_read_events_track * Write shepards.m with new algorithm for nearest neighbors * Use tesselations_stat and tesselations_outwards to clean surfaces * Movies: Use JAVE (Java) * Screen captures: Use Yair Altman functions (in Matlab Central) |
* !FreeSurfer: orig.mgz |
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* Compile stand-alone version: Linux, MacOS * Version with big fonts for live demos * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * Send email to registered users to anounce major improvements * Script tutorials: * Update them to reflect all the recent changes * Script for the time-frequency computation |
* Shortcuts: * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * List of all the keyboard and mouse shortcuts * Equivalents for MacOS |
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* Scouts: Atlases of Tzourio-Mazoyer and Brodman | |
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* Processes: Processing RAW files | |
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* Temporary folder * How to export sources for analysis in SPM |
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* MNE sample dataset | |
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* MRI segmentation with !FreeSurfer => David Wheland | * Epilepsy / spike analysis |
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* Display the "What's new" page after downloading new version of brainstorm | |
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== Unsolved problems == * Surfaces: * Influence of the software used to extract surfaces (!BrainVisa, !BrainSuite, !FreeSurfer) * Type of cortex surface to use: grey/white, grey/csf, midsurface ? * How to get good surfaces for BEM ? * Group analysis: * 1) localization on individual brain + interpolation on MNI brain ? * 2) localization directly on MNI brain ? * Normalize amplitudes across different subjects / runs ? * Online documentation of forward and inverse methods |
== Geeky programming details == * Cleaning surfaces: should work with atlases * Send OpenGL bug report to the Mathworks * Hide Java panels instead of deleting them * mri2scs: convert arguments to meters * Zip files created cannot be open with !WinZip * OpenGL options: {none, software, hardware} * Bug: Scout without overlay, adapt scale for each graph when "Uniform amplitude" 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) * 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) * Write shepards.m with new algorithm for nearest neighbors * Use Matlab Coder to compile / optimize some processes * Optimize calls to bst_get, now study and subject have necessarily the same folder name |
What's next
A roadmap to the future developments of Brainstorm.
Current topics
Data acquisition
- Improve the acquisition of the head points and the registration MEG / MRI
Real-time processing and display (based on FieldTrip realtime module)
- Support for intra-cranial recordings
Pre-processing
- Correction for head movements (using the continuous head localization coils)
Source modeling
- Computation of equivalent current dipoles
- Display results of CTF SAM beamformer
Functionnal connectivity
Integration of different metrics to study the brain connectivity:
Correlation, coherence, Granger causality, phase locking value- Development of new ways to represent the connectivity between sensors or brain regions
Data management
- Filter the display of the tree by type / name / tag
Large scale analysis
- Parallel processing: Reduce the computation times using the parallel processing toolbox
- Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters
Recordings
- RAW file viewer:
- Pre-load next page of recordings
- Allow multiple RAW windows
- 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 cale 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
- Imported recordings: Offer the same interface as the RAW viewer:
- Scroll bar
- Events viewer / editor
- Re-epoch (import from files in database)
- SSP
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
- Calculation and use of p-values for the metrics
- Trial analysis: Concatenations rather than averages for most metrics
- Optimize bst_coherence
- 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
- Use little squares
- Little squares with scout color instead of point
- Max distance slider: useless
- Event-related coherence?
Processes
- Time-frequency:
- Stat computed on time-frequency data
- Validate all the operations on the time-freq files (check for mixed Measures)
- Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
- Scouts values for timefreq on surfaces
- How to combine 3 orientations for unconstrained sources
- Display logs as negative
- 2D Layout in spectrum
- Make much faster and more memory efficient (C functions coded by Matti ?)
- Parallel processing: Use parfor
- Distributed processing:
- Version of Brainstorm that can run without JAVA
- Use the BIC/MEG cluster from the pipeline interface (PSOM, P.Bellec)
- SSP:
Display warning if changing the ChannelFlag while there is a Projector applied
- When processing multiple files: waitbar is not behaving well
- Average:
- Remember how many trials were used per channel
- By subject AND condition
- Save standard deviation
- Display standard deviation as a halo around the time series
- Co-registration of MEG runs:
- SSP: Group projectors coming from different files
- Finish validation of the method
- Apply to continuous recordings for correcting for head movements (using head position coils)
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
- Project sources:
- Adapt smooth factor to the number of vertices
- Number of neighbors to consider = average number of neighbors in the target mesh.
- Compute by small time blocks
- Noise covariance matrix:
- 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
Use the FreeSurfer subject co-registration (downsample: keep the correspondance)
- Import / registration:
- Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...)
- Auto-reorientation of MRI after selected NAS / LPA / RPA
- Major bug when importing surfaces for an MRI that was re-oriented manually
- ICBM brain
- MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab
- ICBM average surfaces + atlas
- Using CIVET pipeline for extracting surfaces
- Clustering cortex: Dimitrios, David, Yu-Teng
Statistics
- Stat on scouts / clusters / "matrix"
- ANOVA: Use LENA functions
- Output = 1 file per effect, all grouped in a node "ANOVA"
- Display several ANOVA maps (from several files) on one single figure, using a "graphic accumulator", towards which one can send any type of graphic object
- Permutation tests:
- t-test only (wilcoxon? sign-test?): paired, equal var, unequal var
- nb permutations ~ 1000
- maximum statistic over "time" or "time and space"
- Permutations / clustering: cf fieldtrip
Threshold in time: keep only the regions that are significative for contiguous blocks of time, or over a certain number of time points
=> Process that creates a static representation of a temporal window
Input / output
- MRI: MINC format
- 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)
- Define scouts from SPM / Analyze 3D masks
FreeSurfer: orig.mgz
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
Anatomy: Segmentation with FreeSurfer
- First steps: Brainstorm preferences
- Headmodel: explain the fields + how to get the constrained leadfield
- Coordinate sytems: How to convert between the different coordinates systems in scripts
- Sources: Modelized data
- Sources: theshold min. size (not documented yet)
- Processes: Describe all the processes
- Processes: How to write your own processes (user folder for processes)
- Import raw recordings: Add "detect bad trials/channels" in the pipeline
- Temporary folder
- 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
Geeky programming details
- Cleaning surfaces: should work with atlases
- Send OpenGL bug report to the Mathworks
- Hide Java panels instead of deleting them
- mri2scs: convert arguments to meters
Zip files created cannot be open with WinZip
- OpenGL options: {none, software, hardware}
- Bug: Scout without overlay, adapt scale for each graph when "Uniform amplitude" 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)
- 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)
- 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