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

== Current topics ==
==== Functionnal connectivity ====
 * Integration of different metrics to study the brain connectivity: <<BR>>Correlation, coherence, Granger causality, phase locking value
 * Development of new ways to represent the connectivity between sensors or brain regions

==== EEG / epilepsy / intra-cranial recordings ====
 * New tools for exploring EEG recordings (custom montages, faster viewer)
 * Full EEG/epilepsy online tutorial
 * Editing the position of intracranial electrodes in the MRI viewer

==== Source modeling ====
 * Computation of equivalent current dipoles
 * Beamformers

==== 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

<<BR>><<BR>><<BR>>

== Recordings ==
 * RAW file viewer:
  * Pre-load next page of recordings
  * Allow multiple RAW windows(columns display)
  * Screen setups: save configuration of windows
  * Time scale: define in fixed s/mm (like the CTF tools)
  * Secondary windows: display length of time selection
  * If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
  * Documentation: Add definition of bad segments
  * Set the ampliude scale for the time series
  * CTRL+S : Save modifications
 * RAW processing:
  * Make it work for all the file formats(at least bandpass filter)
  * Events: advanced process for recombining. Example:  http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
 * Improve interface for SSP on imported recordings
 * 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:
  * Define and display in the MRI viewer
 * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)
 * 2D Layout for multiple conditions

== Connectivity ==
 * Figures: interaction with sensor selection / scouts selections
 * Display NxN as 1xN
 * Adapt colormaps for correlation (min and max properties)
 * PLV: Add a time integration
 * Work on progress bars
 * Circle plot:
  * Display Neuromag sensors
 * Event-related coherence?

== Processes ==
 * Time-frequency:
  * 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 ?)
 * Distributed processing:
  * Version of Brainstorm that can run without JAVA
 * 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
  * 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<<BR>>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.
 * Optical flow

== Database ==
 * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.

 * Add notes in the folders (text files, visible as nodes in the tree)

 * Screen captures: save straight to the database

== 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 ?
  * 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)
 * Magnetic extrapolation:
  * Do the same thing with EEG
 * 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 ==
 * Scouts:
  * Mix constrained/unconstrained/volume sources, using the "Source model" atlas
  * Display edges in the middle of the faces instead of the vertices
  * Project scouts betweens subjects and between hemispheres
  * Display scouts in a tree: hemisphere, region, subregion
  * Downsample to atlas: allow on timefreq/connect files
 * Generate mixed density surfaces
 * Import / registration:
  * Major bug when importing surfaces for an MRI that was re-oriented manually
 * Use mid-gray instead of pial surface?

== 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
 * t-test on volume sources
 * Create icons for Stat/PAC, Stat/Sprectrum, etc.

== Input / output ==
 * EEG File formats:
  * EEG !CeeGraph
  * EGI: Finish support for epoched files (formats 3,5,7)
 * !FieldTrip structures: In / Out
 * BCI2000 Input (via EEGLAB plugin)

== 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
  * First steps: Brainstorm preferences
  * Headmodel: explain the fields + how to get the constrained leadfield
  * Sources: Modelized data
  * Sources: theshold min. size (not documented yet)
  * Processes: Describe all the processes
  * Import raw recordings: Add "detect bad trials/channels" in the pipeline
  * Temporary folder
 * Advanced tutorials:
  * EEG (How to import an EEG cap)
  * Epilepsy / spike analysis

== Geeky programming details ==
 * Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal
 * Hide Java panels instead of deleting them
 * mri2scs: convert arguments to meters
 * Waitbars: 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)
 * Optimize calls to bst_get, now study and subject have necessarily the same folder name
 * Stat files: store tmap or pmap, not both
 * Progress bar with different levels (to handle sub-processes)
 * Progress bar: make work correctly with RAW on resting tutorial
 * Line smoothing / anti-aliasing (time series figures)