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Revision 10 as of 2011-12-13 14:46:59

What's next

A roadmap for the future developments of Brainstorm.

Next six months

Pre-processing

  • Extend processing of continuous CTF files to all file formats
  • 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
  • Make all the main operations available in the pipeline editor

File formats

  • MRI: MINC
  • EEG: Stellate
  • EEG: Brain Products / BrainAmp

  • Read and display NIRS recordings
  • CTF SAM Beamformer results

Functionnal connectivity

  • Implementation of methods developed at USC



Details of those features

  • 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
    • When processing multiple files: waitbar is all messed up
    • Tune parameters for the automatic detection of heartbeats and eye blinks
    • Write documentation
  • RAW file viewer:
    • Buttons for changing scales (time + amplitude)
    • Add tooltips to all the buttons / shortcuts
    • 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 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)
  • 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
  • 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

Other

  • Stat on scouts / clusters / "matrix"
  • Average:
    • Remember how many trials were used per channel
    • By subject AND condition
  • Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions)
  • GUI: Save configuration of windows (per protocol)
  • MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
  • Sources on surface: Display peak regions over time (time = color) => A.Gramfort

  • 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)

Source modeling

  • Inverse:
    • Stable LCMV Beamformer
    • MUSIC
  • Unconstrained sources:
    • 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
    • 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
  • Noise covariance matrix:
    • 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' )

Anatomy

  • Use BrainVISA / FreeSurfer labeling automatically when importing cortex surfaces

  • 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

  • Other processes:
    • Moving average
    • Remove linear trend
    • Power line removal
    • 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

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
    • 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

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

  • EEG File formats:
    • Nihon Kohden
    • EDF+
    • BrainVision / BrainAmp: Get functions from EEGLAB

    • 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 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
  • 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)...
  • 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

Distribution & documentation

  • Version with big fonts for live demos
  • Add Help buttons and menus (in popups, dialog windows...) => Links to the website.

  • List of all the shortcuts
  • 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
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