What's next
A roadmap to the future developments of Brainstorm.
Next six months
Data acquisition
- Improve the acquisition of the head points and the registration MEG / MRI
Pre-processing
- Extend processing of continuous CTF files to all file formats
- Improve detection and correction of artifacts with SSP
- Co-registration of several MEG runs on one single head position
- Make all the main operations available in the pipeline editor
File formats
- MRI: MINC
EEG: Brain Products / BrainAmp
- CTF SAM Beamformer results
Functionnal connectivity
- Implementation of methods developed at USC
Recordings
- RAW file viewer:
- Each RAW viewer window should take a full row of windows (auto-arrange windows)
- Adding events using configurable shortcuts (CTRL+number)
- If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
- Documentation: Add definition of bad segments
- RAW processing:
- Process correctly CTF files saved without the 3rd order grad correction (apply correction before)
- Allow to overwrite RAW files (but with a HUGE warning)
- Update file definition + events if time changes (ex: resample)
- Make it work for all the file formats
- 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 all the EEG caps
- Intracranial electrodes:
- Display in the MRI viewer
- Different data type
- Display time series
- Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)
- Colormaps:
- Create a colormap similar to MNE, where extrema are bright
- Grey out the portion of the colorbars not displayed because of the threshold
Processes
- SSP:
Display warning if changing the ChannelFlag while there is a Projector applied
- When processing multiple files: waitbar is not behaving well
- Write documentation
Complete processing pipeline:
- Import + pre-process
- Sources / head model / noise covariance
- Project sources
- Do not generate errors, stay silent and generate a report log that is shown at the end
- Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions)
- Delete intermediary files
- Complete process of "matrix" file
- Average:
- Remember how many trials were used per channel
- By subject AND condition
- Time-frequency:
- Write script for timefreq tutorial
- Make much faster and more memory efficient (C functions coded by Matti ?)
- Display stat computed on time-frequency data
- Display TF maps separately for the two gradiometers (if not: overlap)
- Source reconstruction by frequency bands
- Scouts on surface / time-freq
- Process selection interface:
- Do not reload the list a each display, but once when starting Brainstorm
- Popup menus: Add a "Process" menu with all the available processes
- Bug when redimensioning window (with more than one process)
- isAvgRef: warning quand process necessite des donnees en AVG REF en entree
- Save "freqband" option when edited from custom processes
- Other processes:
- Moving average
- Max
- Median
- Significance test (Dimitrios, Leo)
- Remove linear trend
- Power line removal
- Bug: gradnorm crashes with bad channels
- Spatial smoothing: check / document parameters
- Sinusoid removal: fix new function
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
- 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:
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)
Anatomy
- BEM surfaces:
- Fix the bumps at the back of the head
- Surface edges: same color as the surface when color was changed
- 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
- Atlas:
Brodmann scouts=> Replace with FreeSurfer labels
Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND
- 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
Use BEM surfaces from FieldTrip
- EEG File formats:
- Stellate
BrainVision / BrainAmp: Get functions from EEGLAB
- Nihon Kohden
- EDF+
EEG CeeGraph
NEUROFILE = COHERENCE EEG/video LongTerm Monitoring => Manfred Spueler
- EGI: Finish support for epoched files (formats 3,5,7)
- Other file formats
- MEG160 (KIT)
CTF: Read STIM channel and generate MarkerFile
- EEGLAB: Apply ICA matrices, get number of trials for AVG files
FieldTrip structures: In / Out
- Output for all the channel file formats
- Define scouts from SPM / Analyze 3D masks
Files > 2Gb: display warnings
Distribution & documentation
- Version with big fonts for live demos
- Automatic update for binary version
- 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
- Send emails 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)
- Ask users to send their channel files, align on Colin, distribute
Geeky programming details
- OpenGL options: {none, software, hardware}
- Bug: Scout without overlay, adapt scale for each graph when "Uniformize" option is unchecked (mixing sources + zscores)
- Waitbars:
- Replace old waitbars with java ones
- Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process)
- Double-click doesn't work well on some Linux workstations
- 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
- Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)...
sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way
- 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