= What's next =
A roadmap to the future developments of Brainstorm.
== Current topics ==
==== Functionnal connectivity ====
* Integration of different metrics to study the brain connectivity: <
>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
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== 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 amplitude scale for the time series
* CTRL+S : Save modifications
* Intracranial electrodes: Define and display in the MRI viewer + 3D figures
* RAW processing:
* Make it work for all the file formats (at least bandpass filter + sin removal)
* Events: advanced process for recombining. Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
* 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
* EEG display:<
>
* bst_selections: Add user defined combinations of sensors (eg. "double banana" for EEG)
* Define custom montage
* Re-reference recordings
* 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
* 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
* 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
* Correlation with delays?
* 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 ?)
* Smooth display of TF/PAC maps (option)
* TF scouts: should display average of TF maps
* Artifact detection:
* Detection of bad segments in the RAW files
* Artifact rejection like SPM: if bad in 20%, bad everywhere
* Test difference between adjacent samples
* Distributed processing: 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
* Improve interface for SSP on imported recordings
* Define SSP from one time point
* Show where the attenuation is projected:<
>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
* 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
* Current Source Density (CSD) => Ghislaine<
>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html
* Other processes:
* Detrending
* 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
* Spectrum figure: use bst_selection
== 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)
* 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:
* 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
* Sort scouts by region in process options
* 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<
> => Process that creates a static representation of a temporal window
* t-test on volume sources
* Create icons for Stat/PAC, Stat/Sprectrum, etc.
* One sample t-test across subjects
== 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)
* Export TF maps to SPM / volumes
* EEGLAB import: Selection of conditions in script mode
== Distribution & documentation ==
* Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
* Introduction tutorials:
* Processes: Describe all the processes
* 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)
* 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
== Current bugs ==
* Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)
* 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 for reports never works: Find another solution
* Close figure with coherence results should hide the "frequency" slider
== 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
* bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
* Shared kernels: do the "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
* Line smoothing / anti-aliasing (time series figures)
* Optimize reload time