= What's next =
A roadmap to the future developments of Brainstorm.
== Current topics ==
==== Source modeling ====
* Implementation of a new unified minimum norm/beamformer framework (work in progress)
==== Statistics ====
* Implementation of new parametric and non-parametric tests (work in progress)
==== Documentation ====
* Standard workflows for different types of data and experiments (work in progress)
==== Functional connectivity ====
* Significance thresholding of the connectivity matrices (not started)
==== Computation ====
* Removing the dependence to the Java interface to run in headless mode (not started)
* Interacting directly with distributed computing systems (not started)
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== Recordings ==
* 2D topographies:
* Nicer topographies with circle around 2DDisc (similar to EEGLAB plots)
* Standardized plots (using FieldTrip .lay files?)
* Aligned on the midline at least
* Contour lines sometimes messed up with Elekta recordings
* Make the surface on which the values are interpolated simpler
* MEG/EEG registration: Apply the same transformation to multiple runs
* 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: Change the category of a selected event easily, instead of deleting/marking new
* 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 (bad for Hilbert as well)
* Or allow the users to edit the LowStop parameter in bst_bandpass.
* Show easily recordings maximum/values in the file viewer
== Interface ==
* Start Brainstorm without Java (-nodesktop)
* Generalize the user of the units (field .Units): Rewrite processes to save the units correctly
* 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
* Smooth display from figure_image (ERPimage, raster plot...)
== Connectivity ==
* Thresholding the connectivity matrices
* t-tests on connectivity measures
* Check why our Hilbert implementation has huge edge effects
* Connectivity on unconstrained sources: how to group the three orientations?
* 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:
* Does not display negative values correctly (correlation or difference of coherence)
* 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)
* NxN on sensors: does not place the sensors correctly in space
* 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
* PAC maps: Display all sensors at once (like TF and DynamicPAC)
* Time-resolved correlation/coherence: Display as time bands
* 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?
* Connect NxN: Display as time series > Display warning before trying to open too many signals
== Processes ==
* Optimize pipeline editor speed: Opening the window and the showing menu "Add process" are slow
* ICA:
* Exploration: Add window with spectral decomposition (useful for muscle artifacts)
* Comparison JADE/Infomax: <
> 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<
>Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )<
>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)
* Use FastICA (algo crashing)
* Understand why EEG/Epilepsy tutorial data crashes if we don't limit the number of components
* Add components preselection: Correlation with EOG/ECG
* Import ICA matrices available in EEGLAB .set files
* Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
* Allow processes in Python and Java
* SSP:
* Display warning if changing the ChannelFlag while there is a Projector applied
* Show where the attenuation is projected:<
>(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 (frequency resolution instead of window length)
* Allow running on source files attached to continuous files (needs a lot of rewriting)
* 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
* Allow the to stack to Process2 together (file selection + test): Add a number of outputs for each process2 (1 or 2), to know if they can be stacked with another process2
* Time-frequency:
* Induced calculation: Avg(Power(TF(trials - Avg(Trials)))): <
>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
* Difference of power displayed in log: problems (Soheila)
* 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.
* 3D figures: Colormaps with "log" option doesn't work
* Extend clusters tab to display of TF to overlay TF signals (Svet)
* TF on scouts: Add progress bar when extracting all the scouts time series (can be long)
* Artifact detection:
* Artifact rejection like SPM: if bad in 20%, bad everywhere
* Test difference between adjacent samples
* Allow the detection on differences of signals (bipolar montages)
* 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)
* Use field process field "Group" to separate Input/Processing/Output options
* Use new Matlab functions: movmean, movsum, movmedian, movmax, movmin, movvar, movstd
== Database ==
* Sort files by comment
* MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
* Matrix files:
* Group matrix files => allow to process matrix files by trial types
* Allow to be dependent from other files
* Add notes in the folders (text files, visible as nodes in the tree)
* Screen captures: save straight to the database
* Rename multiple files
* Default headmodel lost when reloaded: Keep selection on the hard drive (in brainstormstudy.mat)
== 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 (scouts or source maps)
* Create scout form maximum doesn't work (menu Sources > Max value)
* Display in MRI doesn't work
* Smooth display: do not smooth subcortical structures
* Export as .nii volume: doesn't work
* 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
* Beamformers from FieldTrip (LCMV, SAM)
* 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 ==
* 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
* Menu head model > Copy to other conditions/subjects (check if applicable first)
* Generate mixed density surfaces
* Optimize computation interpolation MRI-surface (tess_tri_interp)
* Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
* Major bug when importing surfaces for an MRI that was re-oriented manually
* Smooth surface: Fix little spikes to irregularities in the mesh
* Add eyes models to attract eye activity
== ECOG/SEEG ==
* Co-register MRI and CT for electrodes marking in the MRI Viewer
* 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 ==
* t-test/diff_mean between trial groups: better file comments
* 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?
* Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter
* PLS: Partial Least Squares
* In Stat tab: Correction by temporal extension (display only if effect longer than a given input in ms)
== Input / output ==
* FieldTrip integration:
* Import/Export continuous recordings and non-averaged trials.
* Export trials with a trial definition: http://neuroimage.usc.edu/forums/showthread.php?2213
* 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.
* Use new Matlab functions readtable/writetable (2006b): for Excel and text files
== 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:
* EEG/Epilepsy: Rewrite scripts + update contents (with Geneva2015 walkthrough)
* 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
* Script tutorials: ask what folder contains the tutorial datasets
* 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 ==
* Screen capture:
* Bug on Win8/Win10: doesn't capture the correct part of the screen
* Window managers with fading effect: captures the top window
* Image viewer:
* Difficult to get to 100%
* Buggy on some systems
* 2DLayout:
* (TF) Images are too far apart with EEG 20 channels
* (time series) Sometimes the lines are not visible
* (time series) Does not work when DC offset is not removed
* Progress bar:
* Doesn't close properly on some Linux systems
* Focus requests change workspace when processing constantly (Linux systems)
* MacOS bugs:
* Buttons {Yes,No,Cancel} listed backwards
* Record tab: Text of epoch number is too big
* Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
* Matlab bugs:
* Interface looks small on screens with very high resolutions: Reduce the resolution
* Out of memory errors on Win 32bits (restart Matlab)
* Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
* Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG
* in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
* Edit scout in MRI: small modifications cause huge increase of the scout size
* Canolty maps computation: Fix progress bar
== 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
* Optimize MRI viewer with patch() instead of image()