= What's next =
A roadmap for the future developments of Brainstorm.

== Next six months ==

== New interface elements ==
 * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
 * Functionnal connectivity (display: see eConnectome)
 * 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
 * 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
 * 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

== Source modeling ==
 * Inverse:
  * Stable LCMV Beamformer
  * MUSIC
  * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way
 * 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 ==
 * 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

== 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<<BR>> => 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)...
 * Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow)
 * 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)

== 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