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Revision 52 as of 2012-10-19 19:15:37

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 optical recordings: Near-infrared spectroscopy (NIRS)
  • 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
    • 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)
    • Make it work for all the file formats
    • 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:
    • Display in the MRI viewer
    • Different data type
    • Display time series
    • Forward model
  • Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)

Processes

  • Connectivity:
    • Circle plot for NxN interactions
    • Synthetize + plot N sources into n ROIs (requires scout saved in the surfaces)
    • Menu to easily recompute teh sources in ROI form
  • 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:
    • Stocker scouts dans les fichiers de surface
    • Downsample scouts with surfaces
  • 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

  • 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
    • 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
    => 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)
  • Other file formats
    • MEG160 (Yokogawa/KIT)
    • FieldTrip structures: In / Out

  • Define scouts from SPM / Analyze 3D masks

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

  • 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 "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)
  • 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
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