11487
Comment:
|
11370
|
Deletions are marked like this. | Additions are marked like this. |
Line 7: | Line 7: |
* Real-time processing and display (based on FieldTrip realtime module) * Support for optical recordings: Near-infrared spectroscopy (NIRS) * Support for intra-cranial recordings |
|
Line 9: | Line 12: |
* Correction for head movements (using the continuous head localization coils) | |
Line 10: | Line 14: |
* Continuous viewer: Many small improvements to the usability of its interface * Improve detection and correction of artifacts with SSP * Co-registration of several MEG runs on one single head position |
|
Line 15: | Line 16: |
==== File formats ==== * MRI: MINC * EEG: Stellate * EEG: Brain Products / !BrainAmp * Read and display NIRS recordings * CTF SAM Beamformer results |
'''Source modeling''' * Computation of equivalent current dipoles |
Line 25: | Line 23: |
'''Data management''' * Filter the display of the tree by type / name / tag |
|
Line 29: | Line 31: |
* Buttons for changing scales (time + amplitude) * Add tooltips to all the buttons / shortcuts |
* Each RAW viewer window should take a full row of windows (auto-arrange windows) |
Line 38: | Line 39: |
* Make it work for the file formats * 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) |
* Make it work for all the file formats * Imported recordings: Offer the same interface as the RAW viewer: * Scroll bar * Events viewer / editor * Re-epoch (import from files in database) |
Line 46: | Line 47: |
* Standard setups for al the EEG caps | * Standard setups for all the EEG caps * NIRS: * Add new data type * Display of sensors by pairs oxy/deoxy (red/blue), overlaid |
Line 52: | Line 56: |
* Colormaps: * Create a colormap similar to MNE, where extrema are bright * Grey out the portion of the colorbars not displayed because of the threshold |
|
Line 55: | Line 62: |
* 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 * When processing multiple files: waitbar is all messed up * Tune parameters for the automatic detection of heartbeats and eye blinks |
* Display warning if changing the ChannelFlag while there is a Projector applied * When processing multiple files: waitbar is not behaving well |
Line 61: | Line 65: |
* Complete processing pipeline: | * Complete processing pipeline:<<BR>> |
Line 67: | Line 71: |
* Delete intermediary files * Complete process of "matrix" file |
|
Line 70: | Line 76: |
* Co-registration of MEG runs: * Finish validation of the method * Apply to continuous recordings for correcting for head movements (using head position coils) |
|
Line 74: | Line 83: |
* Power spectrum: computation (FFT/welch, or average of TF) + display(f/Power, 2DLayout) | |
Line 81: | Line 89: |
* Popup menus: Add a "Process" menu with all the available processes | |
Line 87: | Line 94: |
* Max * Median * Significance test (Dimitrios, Leo) |
|
Line 95: | Line 105: |
* Filter display of the database explorer (filename, file type, comment...) | |
Line 101: | Line 112: |
* Dipole fitting | |
Line 119: | Line 131: |
* Optimize bst_extrapm.m, add waitbar * Use the noise covariance from the database instead of recomputing it |
|
Line 126: | Line 136: |
* Problem of having inividual trials + averages in the condition => Display warning or not? | |
Line 144: | Line 155: |
* Use BrainVISA / !FreeSurfer labeling automatically when importing cortex surface * Finalize Brodmann scouts |
* Brodmann scouts=> Replace with FreeSurfer labels |
Line 147: | Line 157: |
Line 164: | Line 175: |
* Use BEM surfaces from !FieldTrip | |
Line 177: | Line 189: |
* Gzipped Nifti (new BrainVISA standard) | |
Line 179: | Line 190: |
* Analyze / Nifti: * Fix output function (output MRIs cannot be imported in SPM) * Use correctly field "orient" to align automatically MRI when importing |
|
Line 187: | Line 195: |
* Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * List of all the keyboard and mouse shortcuts |
* 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 |
Line 212: | Line 223: |
* Display the "What's new" page after downloading new version of brainstorm |
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
Real-time processing and display (based on FieldTrip realtime module)
- Support for optical recordings: Near-infrared spectroscopy (NIRS)
- Support for intra-cranial recordings
Pre-processing
- Correction for head movements (using the continuous head localization coils)
- Extend processing of continuous CTF files to all file formats
- Make all the main operations available in the pipeline editor
Source modeling
- Computation of equivalent current dipoles
Functionnal connectivity
- Implementation of methods developed at USC
Data management
- Filter the display of the tree by type / name / tag
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
- Imported recordings: Offer the same interface as the RAW viewer:
- Scroll bar
- Events viewer / editor
- Re-epoch (import from files in database)
- 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
- NIRS:
- Add new data type
- Display of sensors by pairs oxy/deoxy (red/blue), overlaid
- 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
- Co-registration of MEG runs:
- Finish validation of the method
- Apply to continuous recordings for correcting for head movements (using head position coils)
- 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
- 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
- Dipole fitting
- 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