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

== Current topics ==
==== Documentation ====
 * New online tutorials (work in progress)

==== Source modeling ====
 * Implementation of a new unified minimum norm/beamformer framework (work in progress)

==== Functional connectivity ====
 * Significance thresholding of the connectivity matrices (2016)

==== Computation ====
 * Removing the dependence to the Java interface to run in headless mode (not started)
 * Interacting directly with distributed computing systems  (not started)

<<BR>><<BR>>

== Recordings ==
 * Nicer 2D topographies, standardized (using FieldTrip .lay files?)
 * 2DLayout:
  * Use the same standard positions, too much space between sensors (Recordings + TF)
  * Overlay multiple conditions
  * RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
  * Same shortcuts as the raw file viewer (right-click + move for gain)
 * RAW file viewer:
  * Pre-load next page of recordings
  * Events: advanced process for recombining.
  * Example:  http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
 * Bad channels specified at the program level (for sites that have permanent bad channels: AS)
 * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time]
  * Can be done with Matrix > View as image: extract cluster, concatenate for all trials
 * Filtering:
  * Use short FIR filters instead of IIR for bandpass, to limit the ringing
  * Or allow the users to edit the LowStop parameter in bst_bandpass.

 * Show easily recordings maximum/values in the file viewer

== Interface ==
 * Colormaps:
  * Manage multiple custom colormaps
  * Allow brightness/contrast manipulations on the custom colormaps
  * Create a colormap similar to MNE, where extrema are bright
  * Global colormap max: Should get the maximum across all the open files
 * Open new figures as tab (docked in the Figures window)
 * Copy figures to clipboard (with the screencapture function)
 * Removing all the CTRL and SHIFT in the keyboard shortcuts
 * Display warning before opening files that are too big

== Connectivity ==
 * Thresholding the connectivity matrices
 * t-tests on connectivity measures
 * Check why our Hilbert implementation has huge edge effects
 * Connectivity based on band limited power (Sylvain):
  * Compute Hilbert/Bandpass + correlation of the envelopes
  * Bandpass envelopes before computing correlations?
  * Compute Hilbert(sensors) and then project to source space?
 * Multi-tapers?
 * Graph view:
  * Re-write using pure Matlab code and smoothed graphics
  * Fixed scales for intensity sliders
  * Text bigger
  * Too much data in appdata
  * Fixed scales for intensity sliders
  * Add "=" shortcut for having graphs with similar configurations
  * Disable zoom in one region (serious bugs)
 * Coherence:
  * Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
 * Granger:
  * Crashes sometimes: improve stability
  * Re-write and optimize code
  * Add progress bar
 * PLV:
  * Add p-values
  * Remove evoked
  * Optimize code
  * Add time integration
  * Unconstrained sources
 * PAC:
  * Add input TF , to disconnect TF decomposition and PAC computation (Peter)
  * Refine frequency vector of low frequencies
  * How many central frequencies to use in bst_pac?
  * Change filters: no chirplet functions
  * bst_freqfilter: Use nfcomponents like in bst_pac
  * Esther recommended a larger frequency binning of the PAC estimation
 * Other metrics:
  * Coherence by bands: bst_coherence_band_welch.m
  * Granger by bands: bst_granger_band.m
  * Inter-trial coherence
 * Tutorial coherence [1xN] : Reproduce FieldTrip results?

== Processes ==
 * ICA:
  * Exploration: Add window with spectral decomposition (useful for muscle artifacts)
  * Comparison JADE/Infomax: <<BR>> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135
  * Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)
  * Dimension reduction with PCA adds artifacts: Not done by default in EEGLAB<<BR>>Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )<<BR>>Student Carl Leichter detailed this in his thesis
  * S Makeig: Use ICA to select the IC of interest instead of only removing artifacts
  * Display of spectrum for components (PSD/FFT)
 * Distributed processing: Brainstorm that can run without Java
 * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Allow processes in Python and Java
 * Optimize opening time for the menu "Add process"
 * SSP:
  * Display warning if changing the ChannelFlag while there is a Projector applied
  * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
 * Bandpass:
  * Offer option: bst_bandpass_fft / bst_bandpass_filter
  * Rewrite without the forced low-pass filter at Fs/3
  * Show warning when using inappropriate high-pass filter (precision too high)
  * Use FIR filter
 * Spectral flattening (John):
  * ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis

 * PSD:
  * Rewrite to have the same input as coherence

  * Normalize with the total power (TF/sum(TF,3))
 * Remove line noise: http://www.nitrc.org/projects/cleanline
 * Band-limited power envelope
 * Reports:
  * Save as HTML / PDF
  * Do not display the intermediate files
 * Pipeline editor:
  * Add loops over subjects/conditions/trial groups
 * Time-frequency:
  * Induced calculation: Avg(Power(TF(trials - Avg(Trials)))): <<BR>>Add option "Remove evoked response from each trial"
  * Standardize using: diff before calculation + cumsum (checkbox "flatten data")
  * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  * Display logs as negative
  * 2D Layout in spectrum
  * Make much faster and more memory efficient (C functions coded by Matti ?)
  * TF scouts: should display average of TF maps
  * Impossible to keep complex values for unconstrained sources
  * Pad short epochs with zero values for getting lower frequencies
  * Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead.
 * Artifact detection:
  * Detection of bad segments in the RAW files (Beth)
  * Artifact rejection like SPM: if bad in 20%, bad everywhere
  * Test difference between adjacent samples
  * Allow the detection on differences of signals (bipolar montages)
 * 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 head movements
 * Resample continuous files
 * 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
 * Simulation:
  * Fix units in simulation processes => no *1e-9 in "simulate recordings"
  * Use "add noise" process from Hui-Ling (in Work/Dev/Divers)

== Database ==
 * Optimize startup speed
 * Start Brainstorm without Java (-nodesktop)
 * Sort files by comment
 * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
 * Group matrix files => allow to process matrix files by trial types

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

 * Screen captures: save straight to the database

 * Rename multiple files

 * Allow matrix files to be attached to other files

== Distributed computing ==
 * Options from FieldTrip:
  * Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer
  * Alternative, with less limitations: http://research.cs.wisc.edu/htcondor/
  * Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine
  * Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub
  * Documentation: http://fieldtrip.fcdonders.nl/faq#distributed_computing_with_fieldtrip_and_matlab
 * PSOM: http://psom.simexp-lab.org/

== Source modeling ==
 * Mixed head models:
  * Project to templates
  * Create scout form maximum doesn't work (menu Sources > Max value)
  * Display in MRI doesn't work
  * Smooth display: do not smooth subcortical structures
 * Dipoles:
  * panel_dipoles: Doesn't work with multiple figures
  * Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates
 * Panel Get coordinates: Add button "find maximum"
 * Stenroos 2014 paper: Include the following methods
  * Inner and outer skull surfaces generator from FieldTrip (needs SPM)
  * Nolte corrected-sphere model (good model re:Alex)
  * Fast BEM models
 * Visualize Beamformer results:
  * Read CTF SAM .svl
  * Display as layers in the MRI viewer
 * Unconstrained sources:
  * Stat and connectivity: what to do? (re-send email John+Sylvain)
 * Overlapping spheres: improve the estimation of the spheres for the frontal lobes
 * Volume grid:
  * Test volume sources with all the subsequent processes (timefreq, stat...)
  * Optimize: 3D display (better than 9x9 cubes)
  * Optimize: vol_dilate (with 26 neighbors)
 * Magnetic extrapolation: Do the same thing with EEG
 * Noise covariance matrix:
  * Display with figure_image()
  * 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
 * EEG Source modeling: Manage references and bipolar montages properly (maybe not necessary)
 * MEG source modeling: Do reconstruction only for a subset of sensors for estimating dipoles?
 * Processes compute head model and sources: Additional option to set the file comment
 * Time-frequency beamformers:
  * Band-pass everything in different frequency bands + Source estimation + TF
  * Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF
 * Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
 * BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
 * Hui-Ling beamformers:
  * More explanations about what is in NAI and Spatial filters
  * Explain that is this is better to study effects extended in time (Ntime > Nsensors)
  * Group LCMV+MCB
  * Condition LEFT median nerve: very bad results
 * Menu Sources > Simulate recordings:
  * Do not close the 3D figures after generating a new file
  * Add a process equivalent to this menu

== Anatomy ==
 * Bug: Head surface generated with Brainstorm is too large
 * MNI coordinates: Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256)
 * Project all sub-cortical structures to default anatomy (check code from Denis S)
 * Add cerebellum to default model generated with "Import FS anatomy"
 * Import MRIs with different resolutions: re-interpolate automatically
 * Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
 * Warping: Scale option has to be fixed, it is currently very unstable
 * Scouts:
  * Display edges in the middle of the faces instead of the vertices
  * Display scouts in a tree: hemisphere, region, subregion
  * Downsample to atlas: allow on timefreq/connect files
  * Sort scouts by region in process options
 * Co-register MRI and CT for electrodes marking in the MRI Viewer
 * Generate mixed density surfaces
 * Major bug when importing surfaces for an MRI that was re-oriented manually
 * Smooth surface: Fix little spikes to irregularities in the mesh
 * Menu head model > Copy to other conditions/subjects (check if applicable first)
 * Add eyes models to attract eye activity

== ECOG/SEEG ==
 * Import/export electrodes positions in MNI/SCS/MRI coordinates
 * Display SEEG+ECOG contacts at the same time
 * Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned

== 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
 * Problem t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo
  * Waiting for test from Dimitrios
  * Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test
  * http://fr.wikipedia.org/wiki/Test_de_Shapiro-Wilk
  * http://stats.stackexchange.com/questions/362/what-is-the-difference-between-the-shapiro-wilk-test-of-normality-and-the-kolmog
  * http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html
  * http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html
  * http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab
 * Stat FieldTrip: impossible to do Abs(Mean(Sources)) => Is it a problem?
 * PLS: Partial Least Squares

== Input / output ==
 * FieldTrip structures: Import/Export continuous recordings and non-averaged trials.
 * EEG File formats:
  * EEG CeeGraph
  * EGI: Finish support for epoched files (formats 3,5,7)
 * BCI2000 Input (via EEGLAB plugin)
 * EEGLAB import:
  * Support for binary AND epoched files (now it's one or the other)
  * Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
 * BST-BIN: Add compression
 * Review raw on all the file formats (ASCII EEG and Cartool missing)
 * gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.

== Distribution & documentation ==
 * Reference tutorials on Google scholar + ResearchGate
 * Cleaning threads on the forum
 * Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
 * Finish existing tutorials:
  * Dipoles
  * Auditory: Finish scripts
  * Group MEM/Epilepsy + Epilepsy tutorials
 * New tutorials:
  * MEG connectome
  * Scrambled faces (SPM/MNE-Python)
  * Coherence (cortico-muscular ?)
  * Intra-cranial recordings
  * Co-register MEG runs (Beth)
 * Missing in the introduction tutorials:
  * Volume scouts
  * Sources: Model evaluation (by simulating recordings)
  * Time-frequency: Description of "log freq scale" option
  * Modify a structure manually: Export to Matlab/Import from Matlab
  * File manipulation: file_short, file_fullpath, in_bst_*...
  * Description of all fields in MRI and surfaces
 * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
 * Missing in page "Cite Brainstorm": Add all the methods used in the software

== Current bugs ==
 * Interface looks small on screens with very high resolutions: Reduce the resolution
 * Workshops:
  * Import anatomy folder: Out of memory on Win 32bits (restart Matlab)
  * Compute head model: Out of memory on Win 32bits
 * Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz)
  * Cannot import two .ds folders at once
  * Colors inverted in the PSD/TF plots (power vs. log)
  * Cannot type the name of a channel in "Detect ECG"
 * Image viewer: Difficult to get to 100%
 * Canolty maps computation: Fix progress bar
 * Smooth TF windows that contain multiple plots
 * Record tab: Text of epoch number is too big on MacOS
 * in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
 * 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
 * Image viewer has some bugs on some systems
 * Screen capture when there is a fading effect in the window manager: captures the window
 * Close figure with coherence results should hide the "frequency" slider
 * Edit scout in MRI: small modifications cause huge increase of the scout size
 * Reports: Text size is too small with Java 1.5 (2006b-2007a)
 * Optimize MRI viewer with patch() instead of image()
 * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
 * 2DLayout (time series):
  * Sometimes the lines are not visible
  * Does not work when DC offset is not removed
 * 2DLayout (TF): Images are too far apart with EEG 20 channels
 * Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
 * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG.

== Geeky programming details ==
 * Hide Java panels instead of deleting them
 * Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)
 * bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
 * Shared kernels: "get bad channels" operation in a different way (reading all the files is too slow)
 * Optimize bst_get:
  * Now study and subject have necessarily the same folder name
  * Replace big switch with separate functions
 * Progress bar:
  * Add different levels (to handle sub-processes)
  * Make work correctly with RAW on resting tutorial
  * Uniformize calls in bst_process/Run
  * Add a "Cancel" button
 * Fix all the 'todo' blocks in the code
 * Replace handle "0" with bst_get('groot')
 * At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame)
 * Error message: Add a link to report directly the bug on the forum
 * in_bst_results (isFull=1): DataFile should be relative