Differences between revisions 389 and 537 (spanning 148 versions)

What's next

A roadmap to the future developments of Brainstorm.

Contents

Coregistration
Recordings
Pre-processing
Reproducibility toolbox
Interface
Database
Connectivity
Processes
Anatomy
Forward modeling
Source modeling
ECOG/SEEG
Statistics
Input / output
Distribution
Documentation
Current bugs
Distributed computing
Geeky programming details

Coregistration

Template channel file on a subject anatomy: Apply the MNI transform
MEG/EEG registration: Apply the same transformation to multiple runs

Recordings

Review signals in time-frequency space
Display CTF coils: Show discs instead of squares
Default montages for EEG (sensor selection)
Sleep scoring wish list (Emily C):
- Configurable horizontal lines (for helping detecting visually some thresholds)
- Mouse ruler: Measure duration and amplitude by dragging the mouse.
- Automatic spindle detector
- https://neuroimage.usc.edu/forums/t/page-overlap-while-reviewing-raw-file-a-way-to-set-to-0/11229/13
RAW file viewer speed:
- Downsample before filtering? (attention to the filter design)
- Add parameter to make the visual downsampling more or less aggressive
- Pre-load next page of recordings
- Keep the filter specifications in memory instead of recomputing for every page
BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)
Simulations: https://github.com/lrkrol/SEREEGA

Pre-processing

Integrate with EYE-EEG (Olaf Dimigen)
- Reproduce tutorial: https://www.eyetracking-eeg.org/tutorial.html
- Create EYE-EEG plugin + processes (Raphael Lambert)
- Process: Detect sacades (extended events) + fixations
- Improved ICA
- Eye-movement related potentials
Add note when rejecting trials: https://neuroimage.usc.edu/forums/t/33686
ICA:
- Exclude bad segments (Nathalie G)
- Add Alex's suggestions: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4
- Automatic classification: ICLabel: https://neuroimage.usc.edu/forums/t/automatic-eeg-ic-ica-classification-for-brainstorm/33785
- Add methods: SOBI, Fastica, AMICA/CUDICA/CUDAAMICA (recommended by S Makeig)
- Why doesn't the ICA process converge when using 25 components in the EEG tutorial?
- Add an option to resample the signals before computing the ICA decomposition
- Exploration: Add window with spectral decomposition (useful for muscle artifacts)
- Export IC time series (and then compute their spectrum): solves the problem above
- Comparison JADE/Infomax:
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135
- 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
- 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)
- ICA+machine learning: https://www.ncbi.nlm.nih.gov/pubmed/28497769
- Automated artifact rejection: https://arxiv.org/abs/1612.08194
- Use EYE-EEG: EEGLAB toolbox for eye-tracker guided ICA (Olaf Dimigen): http://www2.hu-berlin.de/eyetracking-eeg/
SSP:
- Display warning if changing the ChannelFlag while there is a Projector applied

Reproducibility toolbox

Generate fully reproducible scripts, including all the interactive/graphical parts
Record all GUI actions as script calls
Import window: Add button to create the corresponding processing pipeline (to generate script or to edit additional options)
Adding the list of plugins to the reports (optionnal or foldable)
Better provenance: History fields, uniform file names...
Improving the pipeline editor to handle loops over data files or subjects

Interface

Add a warning when computing a forward model with > 100000 sources (check selection)
Colormaps: Global colormap max: Should get the maximum across all the open files
Snapshot:
- Save as image / all figures (similar to Movie/all figure)
- Copy figures to clipboard (with the screencapture function)
Contact sheets & movies: use average of time windows instead of single instants, for each picture.
Contact sheets: Allow explicit list of times in input (+ display as in MNE-Python with TS)

Database

Save iHeadModel somewhere in the datbase structure
Generalize the use of the units (field .DisplayUnits)

Connectivity

Thresholding and stat tests for connectivity matrices:
- Panel Display: Show only the top N% measures
- Misic: https://www.nature.com/articles/s41583-022-00601-9
Connect NxN display:
- Graph on sensors: does not place the sensors correctly in space
- Display as image: Add legend of the elements along X and Y axis
- Display as time series: Display warning before trying to open too many signals
- Optimize display: use surface() instead of line() for links? (as in figure_3d/PlotFibers)
Time-resolved correlation/coherence: Display as time bands

Processes

Add MNE-Python functions:
- scikit-learn classifiers
- BEM single layer (John wants to test it)
- ICA: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4
- https://neuroimage.usc.edu/forums/t/best-way-to-export-to-mne-python/12704/3
- Reproduce other tutorials / examples
- Sensitivity maps
- Point-spread functions (PSFs) and cross-talk functions: https://mne.tools/stable/auto_examples/inverse/plot_psf_ctf_vertices.html#sphx-glr-auto-examples-inverse-plot-psf-ctf-vertices-py
- Spatial resolution metrics in source space:
  https://mne.tools/stable/auto_examples/inverse/plot_resolution_metrics.html#sphx-glr-auto-examples-inverse-plot-resolution-metrics-py
- Change the graphic renderer from Matlab
Chronux toolbox : http://chronux.org/
Add FieldTrip functions:
- ft_sourceanalysis:
  - Check noise covariance
  - Check all the options of all the methods
  - Single trial reconstructions + noise covariance?
  - Filters?? http://www.fieldtriptoolbox.org/example/common_filters_in_beamforming
  - Beamformers: Save ftSource.avg.mom
    http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo
  - http://www.natmeg.se/ft_beamformer/beamformer.html
  - http://www.fieldtriptoolbox.org/tutorial/beamformingextended
  - Baseline? Two inputs?
- ft_prepare_heamodel: Add support from BEM surfaces from the Brainstorm database
- Freqanalysis: ITC
- ft_volumereslice: http://www.fieldtriptoolbox.org/faq/how_change_mri_orientation_size_fov
- ft_freqanalysis
- ft_combineplanar
Optimization:
- Test speed for writing files:
  https://undocumentedmatlab.com/articles/improving-fwrite-performance
- Use CUDA for speeding up some operations (filtering, wavelets, etc)
- Use Matlab Coder to optimize: Wavelets, bandpass filter, sinusoid removal
Pipeline editor:
- Bug: After "convert to continuous", the time of the following processes should change
- Add loops over subjects/conditions/trial groups
- Events: Allow selection from a drop-down list (similar to option "channelname" in panel_process_selection)
ITC: Inter-trial coherence (see MNE reports for group tutorial)
http://www.sciencedirect.com/science/article/pii/S1053811916304232
Remove line noise: http://www.nitrc.org/projects/cleanline
Time-frequency:
- Optimization: bst_timefreq (around l.136), remove evoked in source space: Average should be computed in sensor space instead of source space (requested by Dimitrios)
- Short-time Fourier transform: http://www.mikexcohen.com/lectures.html
- 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.
- When normalizing with baseline: Propagate with the edge effects marked in TFmask
- Allow running TF on montages
- Review continuous files in time-frequency space (for epilepsy)
- Bug when computing TF on constrained and unconstrained scouts at the same time (in mixed head models for instance): uses only the constrained information and doesn't sum the 3 orientations for the unconstrained regions.

Anatomy

ICBM152 update:
- Move out default anatomy from GitHub repository:
- Process with FreeSurfer 7.2 + add FS atlases (Brainnettome, Schaeffer, HCP...)
- Add volume atlases (+ reimport ASEG as volatlas)
- Add facemask => Use for defacing with any MNI registration
- Add T2?
BEM surfaces: Deform fieldtrip BEM surfaces from ICBM152 to subject space with MNI coordinates?
Simple-brain-plot: https://github.com/dutchconnectomelab/Simple-Brain-Plot
MRI segmentation:
- SimNIBS: Replace HEADRECO with CHARM (headreco will be removed in SimNIBS 4)
MNI normalization: More options:
- DARTEL / SHOOT
- BrainSuite (wait for Anand)
MRI Viewer:
- Pan in zoomed view (shift + click + move?)
- Zoom in/out with mouse (shift + scroll?)
- Ruler tool to measure distances
- Display scouts as additional volumes
- Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
  Or use inpolyhedron to get a surface mask and then erode it to get the volume envelope
- Surface>Volume interpolation: Use spm_mesh_to_grid instead of tess_tri_interp
Defacing:
- https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html
- Removing MNI face mask using MNI coordinates
Atlas switch in 3D MRI figures
Bug import anatomy: Requested nVert > high-resolution cortex surface: Creates an empty cortex_0V
BrainSuite:
- Use same colors for left and right for anatomical atlases
- Use for volume coregistration (rigid / non-rigid)
- USCBrain: Add default electrodes positions
- Remove BrainSuite1 when not needed anymore
Brain2mesh: Add import of 10-10 positions
Templates for different ages:
Scouts:
- Display edges in the middle of the faces instead of the vertices
- Project from one hemisphere to the other using registered spheres/squares (http://neuroimage.usc.edu/forums/t/how-to-create-mirror-roi-in-the-other-hemisphere/5910/8)
Parcellating volume grids: scikit-learn.cluster.Ward
Geodesic distance calculations:
https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching

Forward modeling

DUNEuro/FEM:
- GeomtryAdapted: Buggy?
- Display differences between leadfields: amplitude of difference (right-click > Compare)
OpenMEEG: Detect bad results + exclude from leadfield
BEM single sphere: Get implementation from MNE
Add eyes models to attract eye activity

Source modeling

Reproduce results in "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
eLORETA instead of sLORETA?
- https://neuroimage.usc.edu/forums/t/compute-eeg-sources-with-sloreta/13425/6
- https://neuroimage.usc.edu/forums/t/loreta-and-source-localization/30525
- "eLORETA algorithm is available in the MEG/EEG Toolbox of Hamburg (METH)": https://www.biorxiv.org/content/biorxiv/early/2019/10/17/809285.full.pdf
- https://github.com/brainstorm-tools/brainstorm3/issues/114
Sensitivity maps: https://mne.tools/stable/auto_examples/forward/plot_forward_sensitivity_maps.html
Point-spread and cross-talk functions (code in MNE-Python):
- https://www.biorxiv.org/content/biorxiv/early/2019/06/18/672956.full.pdf
- https://github.com/olafhauk/EEGMEGResolutionAtlas
Dipoles:
- Display dipoles in MRI viewer
- Project individual dipoles files on a template
- panel_dipoles: Doesn't work with multiple figures
Project sources: Very poor algorithm to project sub-cortical regions and cerebellum
Maximum:
- Menu Sources > Maximum value: Doesn't work with volume or mixed head models
- Panel Get coordinates: Add button "find maximum"
- Sources on surface: Display peak regions over time (time = color) => A.Gramfort
Volume grid:
- Optimize: 3D display (better than 9x9 cubes)
- Optimize: vol_dilate (with 26 neighbors)
Display spectrum scouts (PSD plots when clicking on "Display scouts" on PSD/full cortex)

ECOG/SEEG

Project contact positions across subjects or templates (Marcel)
Right-click on channel file > Project on default anatomy
Display:
- Bad channels: Contacts greyed out instead of ignored (Marcel)
- Display time in H:M:S
- Display curved SEEG electrodes
Create clusters from anatomical labels:
- Identify contacts in a given anatomical region (volume scout, surface mesh, or label in a volume atlas) / allow extracting the signals from all the contacts in an ROI
Automatic segmentation of CT:
- GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
- SEEG DEETO Arnulfo 2015: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0511-6
  - Used routinely at Niguarda Hospital + other hospitals worldwide, reliable tool.
  - To be used with SEEG-assistant/3DSlicer: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1545-8
- ECOG Centracchio 2021: https://link.springer.com/content/pdf/10.1007/s11548-021-02325-0.pdf
  - Classifier on thresholded CT: https://github.com/Jcentracchio/Automated-localization-of-ECoG-electrodes-in-CT-volumes
- SEEG Granados 2018 (no code shared): https://link.springer.com/content/pdf/10.1007/s11548-018-1740-8.pdf
ECOG:
- Project and display contacts on cortex surface should consider the rigidity of the grids: Contacts cannot rotate, and distance between contacts should remain constant across runs
- Method for contacts projection: https://pdfs.semanticscholar.org/f10d/6b899d851f3c4b115404298d7b997cf1d5ab.pdf
- ECOG: Brain shift: When creating contact positions on a post-implantation image, the brain shift should be taken into account for creating images of the ECOG contacts on the pre-op brain => iELVis (http://ielvis.pbworks.com/w/page/116347253/FrontPage)
  Normalization MNI? solutions with FieldTrip?
Detection CEEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect

Statistics

Stat on unconstrained sources?
Stat/time series: Hide lines going down to zero (Dimitrios: https://neuroimage.usc.edu/forums/t/common-source-activation-across-subjects-and-conditions/1152/21)
Cluster stat: Add frequency selection option
ANOVA:
- Write panel similar to Process1 and Process2
- 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
Multivariate stim-response analysis: https://github.com/mickcrosse/mTRF-Toolbox

Input / output

BIDS import:
- Full support for iEEG and EEG
- Read real fiducials (OMEGA) / transformation matrices:
- Read associated empty room:
  - https://github.com/brainstorm-tools/brainstorm3/issues/138
BIDS export:
- Add events tsv, channel tsv, EEG, iEEG
- BIDS-Matlab?
Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284
DICOM converter:
- Add dcm2nii (MRICron)
- Add MRIConvert
SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
EEG File formats:
- XDF: https://github.com/sccn/xdf
- XLTEK: https://github.com/danielmhanover/OpenXLT
- Persyst .lay: https://github.com/ieeg-portal/Persyst-Reader
- Nervus .eeg: https://github.com/ieeg-portal/Nervus-Reader
- Biopac .acq: https://github.com/ieeg-portal/Biopac-Reader
- BCI2000 Input (via EEGLAB plugin)
4D file format:
- Use reader from MNE-Python: mne.io.read_raw_kit (skip Yokogawa slow library)
- Reference gradiometers: Keep the orientation of the first or second coil?
- Reference gradiometers: Add the sensor definition from coil_def.dat
- Validate with phantom recordings that noise compensation is properly taken into account
- The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
- 4D phantom tutorial (JM Badier?)
BST-BIN: Add compression to .bst
MINC MRI: Add support for "voxel to world" transformation (vox2ras) similarly to .nii

Distribution

Java-free Matlab: All references of functions below must be removed
- JavaFrame: screencapture.m (used for screen captures of videos)
- Actxcontrol: Used for video-EEG
  - uihtml + JavaScript callbacks?
  - ActiveX in .NET app?
  - Pure Java framce + VLC java plugin?
  - Other video player?
- Javacomponent:
  - mri_editMask
  - figure_mri
  - process_bandpass
- List .jar files used from Matlab distribution (e.g. dom) => Check all the import calls
Cleanup GitHub repository:
- https://github.com/brainstorm-tools/brainstorm3/issues/473
- Remove ICBM152 default anatomy from repo
- Move external I/O libraries as plugins:
  - mne-matlab
  - CEDS64ML
  - edfimport
  - eeprobe
  - son
  - ricoh
  - yokogawa
  - easyh5

Documentation

All tutorial datasets in BIDS (including introduction tutorials)
Deface the MRIs of all the tutorials
Count GitHub clones in the the download stats
MNE-Python 1.0: Test and update install documentation
Tutorial OMEGA/BIDS:
- Update the organization of derivatives folder (same for ECOG tutorial)
- Add review of literature for the resting state MEG
- Download example datasets directly from the OMEGA repository
New tutorials:
- Other public datasets: https://github.com/INCF/BIDS-examples/tree/bep008_meg/
- EEG/research
- FieldTrip ECOG tutorial: http://www.fieldtriptoolbox.org/tutorial/human_ecog
- Reproduce tutorials from MNE-Python: https://martinos.org/mne/stable/tutorials.html
- Cam-CAN database: https://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/<<BR>>(download new datasets, including maxfiltered files and manual fiducial placements)
- MEG steady-state / high-gamma visual / frequency tagging
- Reproduce results from "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
- Stand-alone ICA tutorial

Current bugs

Image viewer:
- Difficult to get to 100%
- Buggy on some systems
2DLayout:
- (TF) Units are weird with % values
- (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling
Progress bar:
- Doesn't close properly on some Linux systems
- Focus requests change workspace when processing constantly (Linux systems)

Distributed computing

Options from FieldTrip:
- Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer
- Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine
- Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub
- Documentation: https://www.fieldtriptoolbox.org/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/
PSOM: http://psom.simexp-lab.org/
Google: https://www.youtube.com/watch?v=LLMXV3o2FT0
- https://edu.google.com/why-google/case-studies/unc-chapel-hill-gcp/

Geeky programming details

Replace all calls to inpolyhd.m with inpolyhedron.m (10x faster)
Interface scaling: Rewrite class IconLoader to scale only once the icons at startup instead of at each request of an icon (might improve the speed of the rendering of the tree)
Processes with "radio" and "radio_line" options: Replace with "radio_label" and "radio_linelabel"
Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)

-  ⇤ ← Revision 389 as of 2018-03-15 10:07:35 → 
  Size: 27351
  Editor: FrancoisTadel
  Comment:
+   ← Revision 537 as of 2022-06-13 15:13:36 → ⇥
  Size: 20756
  Editor: FrancoisTadel
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-== Current topics ==
==== Electrophysiology ====
 * Spike sorting  interface based on WaveClus

==== Source modeling ====
 * Implementation of a new unified minimum norm/beamformer framework (almost finished)

==== 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)

 * Call MNE-Python and FieldTrip functions from Brainstorm GUI (work in progress)

<<BR>><<BR>>
+== Coregistration ==
 * '''Template channel file on a subject anatomy: Apply the MNI transform '''
 * MEG/EEG registration: Apply the same transformation to multiple runs
-Line 24:
+Line 11:
- * RAW file viewer:<<BR>>
+ * Review signals in time-frequency space
 * Display CTF coils: Show discs instead of squares
 * Default montages for EEG (sensor selection)
 * Sleep scoring wish list (Emily C):
  * Configurable horizontal lines (for helping detecting visually some thresholds)
  * Mouse ruler: Measure duration and amplitude by dragging the mouse.
  * Automatic spindle detector
  * https://neuroimage.usc.edu/forums/t/page-overlap-while-reviewing-raw-file-a-way-to-set-to-0/11229/13
 * RAW file viewer speed:
-Line 29:
+Line 24:
-  * Add field "comment" to markers: For clinicians to add notes (Marcel)
  * Events: Change the category of a selected event easily, instead of deleting/marking new
  * Events: Advanced process for recombining.<<BR>>Example:  http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
 * EEG: Laplacian montage (see doc sent by Jeremy)
 * Bad trials: When changing the status of bad to good: remove the bad segments as well, otherwise it is not processed by processes like the PSD.
 * Review clinical recordings: Reduce the dimensionality of the data with a simple inverse problem, similar to what we do for the magnetic extrapolation ("Regional sources" in BESA, cf S Rampp)
 * MEG/EEG registration: Apply the same transformation to multiple runs
 * 2DLayout:
  * Overlay multiple conditions
  * Does not work when DC offset is not removed
  * Add a proper amplitude scale that gets updated when shift+scroll, to compare figures
  * Update the vertical lines when changing the gain (shift+scroll)
+ * BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)
 * Simulations: https://github.com/lrkrol/SEREEGA

== Pre-processing ==
 * Integrate with EYE-EEG (Olaf Dimigen)
  * Reproduce tutorial: https://www.eyetracking-eeg.org/tutorial.html
  * Create EYE-EEG plugin + processes  (Raphael Lambert)
  * Process: Detect sacades (extended events) + fixations
  * Improved ICA
  * Eye-movement related potentials
 * Add note when rejecting trials: https://neuroimage.usc.edu/forums/t/33686

 * ICA:
  * Exclude bad segments (Nathalie G)
  * Add Alex's suggestions: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4
  * Automatic classification: ICLabel: https://neuroimage.usc.edu/forums/t/automatic-eeg-ic-ica-classification-for-brainstorm/33785
  * Add methods: SOBI, Fastica, AMICA/CUDICA/CUDAAMICA (recommended by S Makeig)
  * Why doesn't the ICA process converge when using 25 components in the EEG tutorial?
  * Add an option to resample the signals before computing the ICA decomposition
  * Exploration: Add window with spectral decomposition (useful for muscle artifacts)
  * Export IC time series (and then compute their spectrum): solves the problem above
  * Comparison JADE/Infomax: <<BR>> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135
  * 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
  * 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)
  * ICA+machine learning: https://www.ncbi.nlm.nih.gov/pubmed/28497769
  * Automated artifact rejection: https://arxiv.org/abs/1612.08194
  * Use EYE-EEG: EEGLAB toolbox for eye-tracker guided ICA (Olaf Dimigen): http://www2.hu-berlin.de/eyetracking-eeg/
 * SSP:
  * Display warning if changing the ChannelFlag while there is a Projector applied

== Reproducibility toolbox ==
 * Generate fully reproducible scripts, including all the interactive/graphical parts
 * Record all GUI actions as script calls
 * Import window: Add button to create the corresponding processing pipeline (to generate script or to edit additional options)
 * Adding the list of plugins to the reports (optionnal or foldable)
 * Better provenance: History fields, uniform file names...
 * Improving the pipeline editor to handle loops over data files or subjects
-Line 44:
+Line 65:
- * Start Brainstorm without Java (-nodesktop)
 * Multiple screens: Add option to set on which display the main bst window should be
 * File filters: Add boolean logic: https://github.com/brainstorm-tools/brainstorm3/issues/68
 * Snapshot: Save as image / all figures (similar to Movie/all figure)
 * Generalize the use of the units (field .DisplayUnits): 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...)
+ * Colormaps: Global colormap max: Should get the maximum across all the open files

 * Snapshot:
  * Save as image / all figures (similar to Movie/all figure)
  * Copy figures to clipboard (with the screencapture function)
-Line 60:
+Line 72:
- * Display CTF coils: Show discs instead of squares
 * Use boundary() instead of conhull() in all the display functions (ie. 2DDisc)
+== Database ==
 * Save iHeadModel somewhere in the datbase structure
 * Generalize the use of the units (field .DisplayUnits)
-Line 64:
+Line 78:
- * Thresholding and stat tests the connectivity matrices
 * Connectivity on unconstrained sources: "Default signal extraction for volume grids should be the time series of  the first principal component of the triplet signals after each has  been zero-meaned" (SB)
 * Display of connectivity graphs:
  * Display as straight lines
  * Recode 2D graphs
  * 3D display with anatomical constrains
 * Use new band-pass filters in bst_connectivity ('bst-hfilter' instead of 'bst-fft-fir')
 * Review by Jan-Mathijs: http://journal.frontiersin.org/article/10.3389/fnsys.2015.00175/full
 * 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?
 * 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)<<BR>>Explore inter-trial approaches (Esther refers to chronux toolbox)
 * Granger:
  * Crashes sometimes: improve stability
  * Check for minimum time window (Esther: min around 500-1000 data points)
  * Re-write and optimize code
  * Add progress bar
 * PLV:
  * Add p-values
  * Remove evoked
  * Optimize code
  * Add time integration
  * Unconstrained sources
  * Add warning when running of short windows (because of filters)
 * 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)
 * Hui-Ling's PAC:
  * https://bsp.hackpad.com/Cross-Frequency-Coupling-cChe95lhDHz
  * https://github.com/NCTU-BSP/MEEG
+ * Thresholding and stat tests for connectivity matrices:
  * Panel Display: Show only the top N% measures
  * Misic: https://www.nature.com/articles/s41583-022-00601-9
  * {{attachment:connect_toolboxes.jpg}}
 * Connect NxN display:
  * Graph on sensors: does not place the sensors correctly in space
  * Display as image: Add legend of the elements along X and Y axis
  * Display as time series: Display warning before trying to open too many signals
  * Optimize display: use surface() instead of line() for links? (as in figure_3d/PlotFibers)
-Line 112:
+Line 88:
- * 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
-Line 120:
+Line 90:
- * Use CUDA for speeding up some operations (filtering, wavelets, etc)
 * Allow processes in Python and Java
-Line 123:
+Line 91:
-  * scikit-learn classifiers: S Marti / G Dehaene
  * Implement data exchange with MNE-Python: write FIF files from Brainstorm and/or pass python objects in memory instead of FIF files
  * SSS/tSSS cleaning
+  * scikit-learn classifiers
  * BEM single layer (John wants to test it)
  * ICA: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4
  * https://neuroimage.usc.edu/forums/t/best-way-to-export-to-mne-python/12704/3
-Line 127:
+Line 96:
+  * Sensitivity maps
  * Point-spread functions (PSFs) and cross-talk functions: https://mne.tools/stable/auto_examples/inverse/plot_psf_ctf_vertices.html#sphx-glr-auto-examples-inverse-plot-psf-ctf-vertices-py
  * Spatial resolution metrics in source space:<<BR>>https://mne.tools/stable/auto_examples/inverse/plot_resolution_metrics.html#sphx-glr-auto-examples-inverse-plot-resolution-metrics-py
-Line 128:
+Line 100:
+ * Chronux toolbox : http://chronux.org/
-Line 138:
+Line 111:
-  * ft_prepare_sourcemodel: Compute MNI transformation (linear and non-linear) => Peter
+  * ft_prepare_heamodel: Add support from BEM surfaces from the Brainstorm database
-Line 140:
+Line 113:
-  * ft_read_atlas('TTatlas+tlrc.BRICK');
-Line 144:
+Line 116:
-  * Allow FieldTrip functions in compiled version
 * Decoding/Classifiers: Faster algorithms (MNE-Python?)
+ * Optimization:
  * Test speed for writing files: <<BR>>https://undocumentedmatlab.com/articles/improving-fwrite-performance
  * Use CUDA for speeding up some operations (filtering, wavelets, etc)
  * Use Matlab Coder to optimize: Wavelets, bandpass filter, sinusoid removal
-Line 149:
+Line 123:
+  * Events: Allow selection from a drop-down list (similar to option "channelname" in panel_process_selection)
-Line 150:
+Line 125:
- * ICA:
  * Why doesn't the ICA process converge when using 25 components in the EEG tutorial?
  * Add an option to resample the signals before computing the ICA decomposition
  * Add a stand-alone tutorial
  * Exploration: Add window with spectral decomposition (useful for muscle artifacts)
  * Export IC time series (and then compute their spectrum): solves the problem above
  * Comparison JADE/Infomax: <<BR>> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135
  * Use faster methods (MNE-Python?)
  * 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)
  * 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)
  * ICA+machine learning: https://www.ncbi.nlm.nih.gov/pubmed/28497769
  * Automated artifact rejection: https://arxiv.org/abs/1612.08194
  * Save IC time series in database
 * 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)
 * Pipeline editor:
  * When computing sources from the pipeline editor: doesn't reselect the options if you click twice on "edit" (works  for minnorm, but not for lcmv)
  * When computing time-frequency/hilbert/psd: Find a way not to force the user to click on Edit
 * Bandpass:
  * Use new filters in all the functions using a bandpass  ('bst-hfilter' instead of 'bst-fft-fir'): process_evt_detect_threshold
  * Weird bug: Filter(import) != Import(Filter) in the HCP tutorial... to investigate
 * Bandpass
 * 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)

  * Use the progress bar

  * Allow display of Avg+StdErr
-Line 190:
+Line 126:
- * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Reports: Click on link reopens exactly the figure
-Line 195:
+Line 129:
-  * Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc
  * Bug: Display logs as negative
  * Bug: 3D figures: Colormaps with "log" option doesn't work
  * Bug: 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
-Line 205:
+Line 130:
-  * Extend clusters tab to display of TF to overlay TF signals (Svet)
-Line 210:
+Line 134:
- * Artifact detection:
  * Artifact rejection like SPM: if bad in 20%, bad everywhere
  * Test difference between adjacent samples
 * Events detection: Add option "std" vs "amplitude"
 * 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
 * Other processes:
  * Moving average
  * Max
  * Median
 * 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
 * Process ft_prepare_heamodel: Add support from BEM surfaces from the Brainstorm database

== Database ==
 * Add buttons to sort files: by name, by comment, by date
 * 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)

 * protocol.mat can be too big: do not store the results links in it (and recreate when loading)- http://neuroimage.usc.edu/forums/t/abnormally-slow-behavior/2065/10

== 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/
 * Various initiatives: http://samirdas.github.io/Data_sharing.html#/

== Source modeling ==
 * Menu head model > Copy to other conditions/subjects (check if applicable first)
 * Menu Sources > Maximum value: Doesn't work with volume or mixed head models
 * Mixed head models: <<BR>>
  * Set loose parameter from the interface
 * Volume grid:
  * Optimize: 3D display (better than 9x9 cubes)
  * Optimize: vol_dilate (with 26 neighbors)
 * Menu Sources > Simulate recordings:
  * Do not close the 3D figures after generating a new file
  * Add a process equivalent to this menu
 * Panel Get coordinates: Add button "find maximum"
 * Dipoles:
  * Project individual dipoles files on a template
  * panel_dipoles: Doesn't work with multiple figures
 * BEM single sphere: Get implementation from MNE
 * 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
 * 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
 * Sources on surface: Display peak regions over time (time = color) => A.Gramfort
 * Calculate ImagingKernel * Gain for a scout
 * 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
 * Keep options for inverse computation
 * OpenMEEG: Post example datasets for the remaining issues:
  * https://github.com/openmeeg/openmeeg/issues/64
  * https://github.com/openmeeg/openmeeg/issues/68
  * Example protocol ECOG: doesn't work
 * Add eyes models to attract eye activity
-Line 303:
+Line 136:
- * Registration:
  * Use the same registration for multiple recording sessions that have already re-registered previously (eg. with MaxFilter)
  * Check templates: MNI transformation and volume atlases for ICBM152 vs Colin27 (loading the AAL atlas as surface or voume scouts do not align well on the ICBM152)
  * Compute non-linear MNI registration instead of linear
  * Select and remove bad digitized head points before automatic coregistration
  * Load the MNE -transf.fif: http://neuroimage.usc.edu/forums/showthread.php?2830
+ * ICBM152 update:
  * Move out default anatomy from GitHub repository:
  * Process with FreeSurfer 7.2 + add FS atlases (Brainnettome, Schaeffer, HCP...)
  * Add volume atlases (+ reimport ASEG as volatlas)
  * Add facemask => Use for defacing with any MNI registration
  * Add T2?
 * BEM surfaces: Deform fieldtrip BEM surfaces from ICBM152 to subject space with MNI coordinates?
 * Simple-brain-plot: https://github.com/dutchconnectomelab/Simple-Brain-Plot
 * MRI segmentation: <<BR>>
  * SimNIBS: Replace HEADRECO with CHARM (headreco will be removed in SimNIBS 4)

 * MNI normalization: More options:
  * DARTEL / SHOOT
  * BrainSuite (wait for Anand)
-Line 313:
+Line 155:
-  * Add keyboard shortcuts to scroll in the three orientations (same in MRI 3D)
-Line 315:
+Line 156:
-  * Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
  * Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
  * Optimize computation interpolation MRI-surface (tess_tri_interp) => spm_mesh_to_grid
 * BrainVISA: Add support for MarsAtlas (Guillaume A)
+  * Render surface envelope in the MRI as a thin line instead of the full interpolation matrix<<BR>>Or use inpolyhedron to get a surface mask and then erode it to get the volume envelope
  * Surface>Volume interpolation: Use '''spm_mesh_to_grid''' instead of tess_tri_interp
 * Defacing:
  * https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html
  * Removing MNI face mask using MNI coordinates
 * Atlas switch in 3D MRI figures
 * Bug import anatomy: Requested nVert > high-resolution cortex surface: Creates an empty cortex_0V
-Line 320:
+Line 164:
-  * Use BrainSuite inner skull for surface generation
-Line 322:
+Line 165:
+  * Use for volume coregistration (rigid / non-rigid)
  * USCBrain: Add default electrodes positions
  * Remove BrainSuite1 when not needed anymore
 * Brain2mesh: Add import of 10-10 positions
 * Templates for different ages:
  * MNI: https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1
  * Pediatric head atlases: https://www.pedeheadmod.net/pediatric-head-atlases-v1-2/

  * https://iopscience.iop.org/article/10.1088/2057-1976/ab4c76
  * https://www.biorxiv.org/content/biorxiv/early/2020/02/09/2020.02.07.939447.full.pdf
  * John Richards: https://www.nitrc.org/frs/?group_id=1361
  * Neurodev database: https://jerlab.sc.edu/projects/neurodevelopmental-mri-database/
  * https://openneuro.org/datasets/ds000256/versions/00002
  * https://osf.io/axz5r/
-Line 324:
+Line 182:
-  * Display scouts in a tree: hemisphere, region, subregion
  * Sort scouts by region in process options
  * Downsample to atlas: allow on timefreq/connect files
-Line 329:
+Line 184:
- * Major bug when importing surfaces for an MRI that was re-oriented manually
 * Smooth surface: Fix little spikes due to irregularities in the mesh
 * Bug: Hide scouts in the preview of the grid for volume head models
+ * Geodesic distance calculations:<<BR>>https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching

== Forward modeling ==
 * DUNEuro/FEM:
  * GeomtryAdapted: Buggy?
  * Display differences between leadfields: amplitude of difference (right-click > Compare)
 * OpenMEEG: Detect bad results + exclude from leadfield
 * BEM single sphere: Get implementation from MNE
 * Add eyes models to attract eye activity

== Source modeling ==
 * Reproduce results in "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
 * eLORETA instead of sLORETA?
  * https://neuroimage.usc.edu/forums/t/compute-eeg-sources-with-sloreta/13425/6
  * https://neuroimage.usc.edu/forums/t/loreta-and-source-localization/30525
  * "eLORETA  algorithm  is  available  in  the  MEG/EEG Toolbox of Hamburg (METH)": https://www.biorxiv.org/content/biorxiv/early/2019/10/17/809285.full.pdf
  * https://github.com/brainstorm-tools/brainstorm3/issues/114
 * Sensitivity maps: https://mne.tools/stable/auto_examples/forward/plot_forward_sensitivity_maps.html
 * Point-spread and cross-talk functions (code in MNE-Python):
  * https://www.biorxiv.org/content/biorxiv/early/2019/06/18/672956.full.pdf
  * https://github.com/olafhauk/EEGMEGResolutionAtlas
 * Dipoles:
  * Display dipoles in MRI viewer
  * Project individual dipoles files on a template
  * panel_dipoles: Doesn't work with multiple figures
 * Project sources: Very poor algorithm to project sub-cortical regions and cerebellum
 * Maximum:
  * Menu Sources > Maximum value: Doesn't work with volume or mixed head models
  * Panel Get coordinates: Add button "find maximum"
  * Sources on surface: Display peak regions over time (time = color) => A.Gramfort
 * Volume grid:
  * Optimize: 3D display (better than 9x9 cubes)
  * Optimize: vol_dilate (with 26 neighbors)
 * Display spectrum scouts (PSD plots when clicking on "Display scouts" on PSD/full cortex)
-Line 334:
+Line 220:
- * Contact positions: Import / set / detect<<BR>>
  * Add history: Save modifications and transformations applied to the channel files (Marcel)
  * ECOG: How to handle cases where not all the grid contacts are in the channel file? (Marcel)
  * Project contact positions across subjects or templates (Marcel)
  * ECOG: Default names of contacts?
 * Editable list of montages shortcuts
 * Automatic segmentation of CT:
  * GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
  * Arnulfo: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0511-6
  * MAP07 / SPM: https://www.epi.ch/_files/Artikel_Epileptologie/Huppertz_2_13.pdf
 * ECOG: Project and display contacts on cortex surface should consider the rigidity of the grids: Contacts cannot rotate, and distance between contacts should remain constant across runs
 * ECOG: Brain shift: When creating contact positions on a post-implantation image, the brain shift should be taken into account for creating images of the ECOG contacts on the pre-op brain => iELVis (http://ielvis.pbworks.com/w/page/116347253/FrontPage)
+ * Project contact positions across subjects or templates (Marcel)<<BR>>Right-click on channel file > Project on default anatomy
-Line 350:
+Line 225:
- * Re-referencing:
  * Create new average reference montages with a specific list of channels, with the possibility to edit the order of the channels (for Jeremy)
  * Closest white reference (Arnulfo)
 * Alternatives to OpenMEEG: SimBio/FieldTrip? Matti Stenroos? NFT/NIST?
+ * Create clusters from anatomical labels:
  * Identify contacts in a given anatomical region (volume scout, surface mesh, or label in a volume atlas) / allow extracting the signals from all the contacts in an ROI
 * Automatic segmentation of CT:
  * GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
  * SEEG DEETO Arnulfo 2015: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0511-6
   * Used routinely at Niguarda Hospital + other hospitals worldwide, reliable tool.
   * To be used with SEEG-assistant/3DSlicer: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1545-8
  * ECOG Centracchio 2021: https://link.springer.com/content/pdf/10.1007/s11548-021-02325-0.pdf
   * Classifier on thresholded CT: https://github.com/Jcentracchio/Automated-localization-of-ECoG-electrodes-in-CT-volumes
  * SEEG Granados 2018 (no code shared): https://link.springer.com/content/pdf/10.1007/s11548-018-1740-8.pdf
 * ECOG:
  * Project and display contacts on cortex surface should consider the rigidity of the grids: Contacts cannot rotate, and distance between contacts should remain constant across runs
  * Method for contacts projection: https://pdfs.semanticscholar.org/f10d/6b899d851f3c4b115404298d7b997cf1d5ab.pdf
  * ECOG: Brain shift: When creating contact positions on a post-implantation image, the brain shift should be taken into account for creating images of the ECOG contacts on the pre-op brain => iELVis (http://ielvis.pbworks.com/w/page/116347253/FrontPage) <<BR>>Normalization MNI? solutions with FieldTrip?
 * Detection CEEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect
-Line 356:
+Line 242:
+ * Stat on unconstrained sources?
 * Stat/time series: Hide lines going down to zero (Dimitrios: https://neuroimage.usc.edu/forums/t/common-source-activation-across-subjects-and-conditions/1152/21)
 * Cluster stat: Add frequency selection option
-Line 357:
+Line 246:
-  * Use LENA functions(?)
+  * Write panel similar to Process1 and Process2
-Line 360:
+Line 249:
- * New process to test for Gaussianity using swtest
 * PLS: Partial Least Squares
 * Simulate recordings with specific properties, for stat validation
 * Quality control before statistics, on condition averages across subjects:<<BR>>mean(baseline)/std(baseline): shows bad subject quickly.
 * Use SurfStat: Impements interesting things, like an analytical  cluster-based p-value correction (Random-field theory which is used in  SPM) - Peter
+ * Multivariate stim-response analysis: https://github.com/mickcrosse/mTRF-Toolbox
-Line 368:
+Line 252:
- * '''XDF import''': Use the EEGLAB plugin, contact Martin Bleichner (Oldenburg)
 * Output .nii have incorrect sform/qform when using the options to downsample the volume of cut the empty slices
+ * BIDS import:
  * Full support for iEEG and EEG
  * Read real fiducials (OMEGA) / transformation matrices:
   * https://groups.google.com/g/bids-discussion/c/BeyUeuNGl7I
   * https://github.com/bids-standard/bids-specification/issues/752#issuecomment-795880992
   * https://github.com/brainstorm-tools/brainstorm3/issues/139
  * Read associated empty room:
   * https://github.com/brainstorm-tools/brainstorm3/issues/138
 * BIDS export:
  * Add events tsv, channel tsv, EEG, iEEG
  * BIDS-Matlab?
 * Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284
-Line 373:
+Line 267:
- * FieldTrip: Import/Export time-frequency:
  * Export: http://neuroimage.usc.edu/forums/t/export-time-frequency-to-fieldtrip/1968
  * Import: http://neuroimage.usc.edu/forums/t/import-time-frequency-data-from-fieldtrip/2644
 * 4D file format:
  * Use reader from MNE-Python: mne.io.read_raw_kit  (doesn't require Yokogawa slow library)
  * Reference gradiometers: Keep the orientation of the first or second coil?
  * Reference gradiometers: Add the sensor definition from coil_def.dat
  * Validate with phantom recordings that noise compensation is properly taken into account
  * References at too far from the head sensors in Marseille 4D system
  * The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
  * 4D phantom tutorial (JM Badier?)
+ * SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
-Line 385:
+Line 269:
-  * EEG CeeGraph
  * EGI: Finish support for epoched files (formats 3,5,7)
+  * XDF: https://github.com/sccn/xdf
-Line 391:
+Line 274:
-  * gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.
 * 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
 * BST-BIN: Add compressionto .bst
 * Review raw on all the file formats (ASCII EEG and Cartool missing)
 * SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
 * Get acquisition date from files: Missing for 4D

== Distribution & documentation ==
 * Compile with FieldTrip and SPM
 * Add tags to the forum posts for easier listing by topic
+  * BCI2000 Input (via EEGLAB plugin)
 * 4D file format:
  * Use reader from MNE-Python: mne.io.read_raw_kit  (skip Yokogawa slow library)
  * Reference gradiometers: Keep the orientation of the first or second coil?
  * Reference gradiometers: Add the sensor definition from coil_def.dat
  * Validate with phantom recordings that noise compensation is properly taken into account
  * The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
  * 4D phantom tutorial (JM Badier?)
 * BST-BIN: Add compression to .bst
 * MINC MRI: Add support for "voxel to world" transformation (vox2ras) similarly to .nii

== Distribution ==
 * Java-free Matlab: All references of functions below must be removed
  * '''JavaFrame''': screencapture.m (used for screen captures of videos)
  * '''Actxcontrol''': Used for video-EEG
   * uihtml + JavaScript callbacks?
   * ActiveX in .NET app?
   * Pure Java framce + VLC java plugin?
   * Other video player?
  * '''Javacomponent''':
   * mri_editMask
   * figure_mri
   * process_bandpass
  * List .jar files used from Matlab distribution (e.g. dom) => Check all the import calls
 * Cleanup GitHub repository:
  * https://github.com/brainstorm-tools/brainstorm3/issues/473
  * Remove ICBM152 default anatomy from repo
  * Move external I/O libraries as plugins:
   * mne-matlab
   * CEDS64ML
   * edfimport
   * eeprobe
   * son
   * ricoh
   * yokogawa
   * easyh5

== Documentation ==
 * All tutorial datasets in BIDS (including introduction tutorials)
 * Deface the MRIs of all the tutorials
 * Count GitHub clones in the the download stats
 * MNE-Python 1.0: Test and update install documentation
-Line 405:
+Line 317:
+  * Update the organization of derivatives folder (same for ECOG tutorial)
-Line 407:
+Line 320:
- * New tutorials:
  * Visual group Henson/Wakeman tutorial: Use the BIDS version<<BR>>https://github.com/INCF/BIDS-examples/tree/bep008_meg/ds000117
+ * New tutorials: <<BR>>
-Line 410:
+Line 322:
-  * Rat PAC + high gamma (Soheila)
-Line 413:
+Line 324:
-  * FieldTrip cortico-muscular coherence tutorial: http://www.fieldtriptoolbox.org/tutorial/coherence
-Line 416:
+Line 326:
- * MEG steady-state / high-gamma visual / frequency tagging
 * BIDS-EEG example datasets
 * Intra-cranial recordings (Marcel, Jeremy?)
 * Stand-alone ICA tutorial
 * Co-register MEG runs (Beth)

 * Move all the files to download on the cloud for faster download everywhere in the world
 * Provide secure way of sending password over HTTPS for:
  * Account creation
  * Forum exchanges
  * org.brainstorm.dialog.CloneControl
 * Workflows FieldTrip: http://www.fieldtriptoolbox.org/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip
 * Reference tutorials on Google scholar + ResearchGate
 * Count GitHub clones in the the download stats
 * Google Analytics: Create template and update the section of the Community page

 * Missing in page "Cite Brainstorm": Add all the methods used in the software
 * Deface the MRIs of all the tutorials
 * Compiled R2016b: Color picker doesn't work (for changing surface color for instance)
+  * MEG steady-state / high-gamma visual / frequency tagging
  * Reproduce results from "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
  * Stand-alone ICA tutorial
-Line 438:
+Line 331:
- * Screen capture:
  * Bug on Win8/Win10: doesn't capture the correct part of the screen
  * Window managers with fading effect: captures the top window
-Line 450:
+Line 340:
- * 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
 * 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
+== Distributed computing ==
 * Options from FieldTrip:
  * Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer
  * Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine
  * Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub
  * Documentation: https://www.fieldtriptoolbox.org/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/
 * PSOM: http://psom.simexp-lab.org/
 * Google: https://www.youtube.com/watch?v=LLMXV3o2FT0
  * https://edu.google.com/why-google/case-studies/unc-chapel-hill-gcp/
-Line 462:
+Line 352:
- * bst_bsxfun: After 2016b, we can use directly the scalar operators (./ .* ...) instead of bsxfun. Update bst_bsxfun to skip the use of bsxfun when possible.
+ * Replace all calls to inpolyhd.m with inpolyhedron.m (10x faster)
-Line 464:
+Line 354:
- * Hide Java panels instead of deleting them
-Line 467:
+Line 356:
- * 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
 * Error message: Add a link to report directly the bug on the forum

Software

Users

Development

What's next

Coregistration

Recordings

Pre-processing

Reproducibility toolbox

Interface

Database

Connectivity

Processes

Anatomy

Forward modeling

Source modeling

ECOG/SEEG

Statistics

Input / output

Distribution

Documentation

Current bugs

Distributed computing

Geeky programming details