Differences between revisions 4 and 201 (spanning 197 versions)

What's next

A roadmap to the future developments of Brainstorm.

Contents

Current topics
Recordings
Interface
Connectivity
Processes
Database
Distributed computing
Source modeling
Anatomy
ECOG/SEEG
Statistics
Input / output
Distribution & documentation
Current bugs
Geeky programming details

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)

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
Montages:
- Allow to set the color for each channel separately
- Allow the superposition of channels (NIRS)
- Separators (" : MLC11" already works, could be just " : "), should add an empty space.
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)
- Add support for montages
RAW file viewer:
- Show easily the maximum value at the current time point
- 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
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
Bad channels specified at the program level (for sites that have permanent bad channels: AS)

Interface

Start Brainstorm without Java (-nodesktop)
Generalize the user of the units (field .Units): Rewrite processes to save the units correctly
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
Stat 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
- EEGLAB recommends ICA + trial rejection + ICA again: Impossible right now with Brainstorm
  (http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA)
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
Pipeline editor:
- Add loops over subjects/conditions/trial groups
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: 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
Calculate ImagingKernel * Gain for a scout
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 due 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

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)
FieldTrip implementation:
- Add logic of bad channels individually per sensor instead of removing completely all the channels that are marked as bad in at least one trial
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
- Group MEM/Epilepsy + Epilepsy tutorials
New tutorials:
- MEG steady-state / high-gamma visual
- Intra-cranial recordings
- MEG connectome (impossible without the head shapes)
- Scrambled faces (SPM/MNE-Python)
- Coherence (cortico-muscular ?)
- 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
Change of default anatomy does not reset the interpolation matrices in all the subjects.
- After projecting sources once from subject to default anat, the interpolation is saved and not updated. Interpolations need to be removed manually before projecting again on a new template.

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()

-  ⇤ ← Revision 4 as of 2011-12-12 22:47:14 → 
  Size: 11408
  Editor: grumio
  Comment:
+   ← Revision 201 as of 2016-02-25 13:54:34 → ⇥
  Size: 20348
  Editor: FrancoisTadel
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-A roadmap for the future developments of Brainstorm.

== Next six months ==
=== Continuous recordings in native format ===
 * Extend processing of continuous CTF files to all file formats
 * Improve detection and correction of artifacts with SSP
 * Continuous viewer: Many small improvements to the usability of its interface

=== Functionnal connectivity ===
 * Implementation of methods developed at USC
+A roadmap to the future developments of Brainstorm.

<<TableOfContents(2,2)>>

== 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)
-Line 15:
+Line 25:
-== New interface elements ==
+== 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
 * Montages:
  * Allow to set the color for each channel separately
  * Allow the superposition of channels (NIRS)
  * Separators (" : MLC11" already works, could be just " : "), should add an empty space.
 * 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)
  * Add support for montages
 * RAW file viewer:
  * Show easily the maximum value at the current time point
  * 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
 * 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

 * Bad channels specified at the program level (for sites that have permanent bad channels: AS)

== Interface ==
 * Start Brainstorm without Java (-nodesktop)
 * Generalize the user of the units (field .Units): Rewrite processes to save the units correctly
 * 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
 * Stat 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: <<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)
  * 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
  * EEGLAB recommends ICA + trial rejection + ICA again: Impossible right now with Brainstorm<<BR>>(http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA)
 * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Allow processes in Python and Java
-Line 17:
+Line 134:
-  * Write documentation
  * 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
 * RAW file
 * 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
+  * 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 (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
 * 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
  * 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
-Line 27:
+Line 195:
- * 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
+ * Matrix files: 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/
-Line 39:
+Line 215:
- * Inverse:
  * Stable LCMV Beamformer
  * MUSIC
  * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way
+ * 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
-Line 44:
+Line 233:
-  * Define as default
  * Check all the processes
  * Difference and stat should be: norm(A) - norm(B)
+  * Stat and connectivity: what to do? (re-send email John+Sylvain)
-Line 49:
+Line 236:
-  * Scouts 3D
-Line 51:
+Line 237:
-  * Optimize: 3D display (better that 9x9 cubes)
+  * Optimize: 3D display (better than 9x9 cubes)
-Line 53:
+Line 239:
-  * 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
+ * Magnetic extrapolation: Do the same thing with EEG
-Line 63:
+Line 241:
+  * 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?
-Line 64:
+Line 246:
-  * When deploying to other conditions: Apply destination SSP (!NoiseCov = SSP . !NoiseCov . SSP' )
+  * When deploying to other conditions: Apply destination SSP (NoiseCov = SSP.NoiseCov.SSP' )
 * Sources on surface: Display peak regions over time (time = color) => A.Gramfort
 * Calculate ImagingKernel * Gain for a scout
 * 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
-Line 67:
+Line 265:
- * MRI import: auto-reorientation of MRI  after selected NAS / LPA / RPA.
+ * 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
-Line 69:
+Line 281:
- * 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
+ * Smooth surface: Fix little spikes due 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
-Line 111:
+Line 291:
- * ANOVA: Use LENA functions
+ * ANOVA: Use LENA functions(?)
-Line 114:
+Line 294:
- * 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 ==
+ * Problem t-test on unconstrained sources: (convert to flat + Z-score)
 * FieldTrip implementation:
  * Add logic of bad channels individually per sensor instead of removing completely all the channels that are marked as bad in at least one trial
 * 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
-Line 135:
+Line 306:
-  * Nihon Kohden
  * EDF+
  * !BrainVision / !BrainAmp: Get functions from EEGLAB
  * EEG !CeeGraph
  * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler
+  * EEG CeeGraph
-Line 141:
+Line 308:
- * 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
+ * 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
  * Group MEM/Epilepsy + Epilepsy tutorials
 * New tutorials:
  * MEG steady-state / high-gamma visual
  * Intra-cranial recordings
  * MEG connectome (impossible without the head shapes)
  * Scrambled faces (SPM/MNE-Python)
  * Coherence (cortico-muscular ?)
  * 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
 * Change of default anatomy does not reset the interpolation matrices in all the subjects.
  * After projecting sources once from subject to default anat, the interpolation is saved and not updated. Interpolations need to be removed manually before projecting again on a new template.

== Geeky programming details ==
 * Hide Java panels instead of deleting them
 * Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)
-Line 161:
+Line 376:
- * 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)
 * Use Matlab Coder to compile / optimize some processes

== 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
+ * 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()

Software

Users

Development

What's next

Current topics

Source modeling

Statistics

Documentation

Functional connectivity

Computation

Recordings

Interface

Connectivity

Processes

Database

Distributed computing

Source modeling

Anatomy

ECOG/SEEG

Statistics

Input / output

Distribution & documentation

Current bugs

Geeky programming details