|
Size: 11408
Comment:
|
Size: 13223
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| A roadmap for the future developments of Brainstorm. == Next six months == === Continuous recordings in native format === * Extend processing of continuous CTF files to all file formats * Improve detection and correction of artifacts with SSP * Continuous viewer: Many small improvements to the usability of its interface === Functionnal connectivity === * Implementation of methods developed at USC <<BR>><<BR>> == New interface elements == |
A roadmap to the future developments of Brainstorm. == Current topics == ==== 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 ==== * Editing the position of intracranial electrodes in the MRI viewer ==== Source modeling ==== * Computation of equivalent current dipoles * Beamformers ==== Large scale analysis ==== * Parallel processing: Reduce the computation times using the parallel processing toolbox * Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters <<BR>><<BR>><<BR>> == Recordings == * 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 * 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 * 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) == Connectivity == * Tutorial coherence [1xN] * 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 ?) * Smooth display of TF/PAC maps (option) * 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 |
| Line 17: | Line 79: |
| * Write documentation * 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 * RAW file * bst_selections: * Add user defined combinations of sensors (eg. "double banana" for EEG) * Use this to produce "inversed polarity" displayes too (useful in EEG) * Standard setups for al the EEG caps |
* 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) * 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<<BR>>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html * Other processes: * Detrending * 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 == Database == |
| Line 27: | Line 102: |
| * 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) * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab) * Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise) * 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 |
* 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 * PSOM: http://psom.simexp-lab.org/ |
| Line 39: | Line 120: |
| * Inverse: * Stable LCMV Beamformer * MUSIC * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way |
* Compare: dSPM vs. wMNE+zscore * Finish dipole scanning * 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 |
| Line 44: | Line 131: |
| * Define as default * Check all the processes |
* Compute unconstrained and then project on the normal ? |
| Line 47: | Line 133: |
| * Stat and connectivity: what to do? (re-send email John+Sylvain) | |
| Line 53: | Line 140: |
| * Optimize: grid_interp_mri * Magnetic extrapolation: * Do the same thing with EEG * Optimize bst_extrapm.m, add waitbar * Use the noise covariance from the database instead of recomputing it * Project sources: * Adapt smooth factor to the number of vertices * Number of neighbors to consider = average number of neighbors in the target mesh. * Compute by small time blocks |
* Magnetic extrapolation: Do the same thing with EEG |
| Line 63: | Line 142: |
| * 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? |
|
| Line 65: | Line 148: |
| * 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 |
|
| Line 67: | Line 156: |
| * MRI import: auto-reorientation of MRI after selected NAS / LPA / RPA. * Major bug when importing surfaces for an MRI that was re-oriented manually * Finalize Brodmann scouts * Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND * Clustering cortex: Dimitrios, David, Yu-Teng == Processes == * 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 |
* 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? |
| Line 116: | Line 174: |
| * 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 |
|
| Line 122: | Line 183: |
== 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 == |
* 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 == 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_*) |
| Line 135: | Line 199: |
| * Nihon Kohden * EDF+ * !BrainVision / !BrainAmp: Get functions from EEGLAB |
|
| Line 139: | Line 200: |
| * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler | |
| Line 141: | Line 201: |
| * 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 * Define scouts from SPM / Analyze 3D masks * 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 |
* BCI2000 Input (via EEGLAB plugin) * EEGLAB import: Selection of conditions in script mode == Distribution & documentation == * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * Publication list: Folder 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 == * 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) |
| Line 161: | Line 249: |
| * 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)... |
|
| Line 164: | Line 250: |
| * 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) * Use Matlab Coder to compile / optimize some processes == Distribution & documentation == * 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 * Introduction tutorials: * Estimate time to complete each tutorial * Clusters * Anatomy: Segmentation with !FreeSurfer * First steps: Brainstorm preferences * Headmodel: explain the fields + how to get the constrained leadfield * Coordinate sytems: How to convert between the different coordinates systems in scripts * Sources: Modelized data * Sources: theshold min. size (not documented yet) * Scouts: Atlases of Tzourio-Mazoyer and Brodman * Processes: Describe all the processes * Processes: How to write your own processes (user folder for processes) * Processes: Processing RAW files * Import raw recordings: Add "detect bad trials/channels" in the pipeline * Advanced tutorials: * MNE sample dataset * EEG (How to import an EEG cap) * MRI segmentation with !FreeSurfer => David Wheland * How to make and compress a movie (Brainstorm + !VirtualDub + XVid) * Display the "What's new" page after downloading new version of brainstorm * Ask users to send their channel files, align on Colin, distribute == 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 |
* 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
Integration of different metrics to study the brain connectivity:
Correlation, coherence, Granger causality, phase locking value- Development of new ways to represent the connectivity between sensors or brain regions
EEG / epilepsy / intra-cranial recordings
- Editing the position of intracranial electrodes in the MRI viewer
Source modeling
- Computation of equivalent current dipoles
- Beamformers
Large scale analysis
- Parallel processing: Reduce the computation times using the parallel processing toolbox
- Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters
Recordings
- RAW file viewer:
- Pre-load next page of recordings
- 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
- 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
- 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]
- 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 ?)
- Smooth display of TF/PAC maps (option)
- 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.html- Other processes:
- Detrending
- 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
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
- Compare: dSPM vs. wMNE+zscore
- Finish dipole scanning
- 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
Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
- Publication list: Folder 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
- 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