Differences between revisions 273 and 495 (spanning 222 versions)

What's next

A roadmap to the future developments of Brainstorm.

Contents

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

Recordings

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
MEG/EEG registration: Apply the same transformation to multiple runs
Create heat maps: Maybe with matlab function heatmap?
BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)

Interface

Add a warning when computing a forward model with > 100000 sources (check selection)
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
- Global colormap max: Should get the maximum across all the open files
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)
Display CTF coils: Show discs instead of squares
Progress bar: Add a "Cancel" button
Error message: Add a link to report directly the bug on the forum
Reorganize menus (Dannie's suggestion):

Connectivity

Thresholding and stat tests for 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)
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
Time-resolved correlation/coherence: Display as time bands
Weighted Phase Lag Index (WPLI)
Coherence: Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
Explore inter-trial approaches (Esther refers to chronux toolbox)
Granger: Check for minimum time window (Esther: min around 500-1000 data points)
PLV:
- Remove evoked
- Add time integration
- Unconstrained sources
- Add warning when running of short windows (because of filters)

Processes

Plugin manager:
- Export all the software environment to a .zip file (brainstorm + all plugins)
Generate fully reproducible scripts, including all the interactive/graphical parts:
- Saving all the interactive operations as process calls
- Improving the pipeline editor to handle loops over data files or subjects
- Keeping a better track of the provenance of all the data (History field, and maybe more uniform file names)
Add MNE-Python functions:
- scikit-learn classifiers
- 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
- 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
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:
- 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
ICA:
- Add Alex's suggestions: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4
- 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
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
- Bug: Display logs as negative
- Bug: 3D figures: Colormaps with "log" option doesn't work
- Bug: Difference of power displayed in log: problems (Soheila)
- TF scouts: should display average of TF maps
- Impossible to keep complex values for unconstrained sources
- 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.
Use field process field "Group" to separate Input/Processing/Output options
Use new Matlab functions: movmean, movsum, movmedian, movmax, movmin, movvar, movstd

Database

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
Rename multiple files
Default headmodel lost when reloaded: Keep selection on the hard drive (in brainstormstudy.mat)
Auto-save:
- 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
- Improve auto-save: add tracking file next to protocol.mat, do not save all the time, only when closing app, and reload protocol at stratup if tracking file is still there

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/

Source modeling

Unconstrained to flat: Default PCA for stat and connectivity?
Sensitivity maps: https://mne.tools/stable/auto_examples/forward/plot_forward_sensitivity_maps.html
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
Use eLORETA instead of sLORETA?
https://neuroimage.usc.edu/forums/t/compute-eeg-sources-with-sloreta/13425/6
- "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
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:
- 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 (algorithm to fit surfaces should be imrpoved)
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:
- Bug when displaying interpolated in MRI viewer
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"
BEM single sphere: Get implementation from MNE
Unconstrained sources:
- Stat and connectivity: what to do? (re-send email John+Sylvain)
Sources on surface: Display peak regions over time (time = color) => A.Gramfort
Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
Add eyes models to attract eye activity
Display spectrum scouts (PSD plots when clicking on "Display scouts" on PSD/full cortex)

Anatomy

FastSurfer: https://deep-mi.org/research/fastsurfer/
SimNIBS: Replace HEADRECO with CHARM (headreco will be removed in SimNIBS 4)
Infant templates: Add electrodes positions (at least 10-10)
Neurodev MRI database: https://jerlab.sc.edu/projects/neurodevelopmental-mri-database/
Multi-Scale Brain Parcellator (Lausanne2008):
Registration:
- Getting electrode positions from 3D scanners: https://sccn.ucsd.edu/wiki/Get_chanlocs
- GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
- Use the same registration for multiple recording sessions that have already re-registered previously (eg. with MaxFilter)
- When linking multiple EEG recordings including 3D positions, do the registration only once and copy it to all the runs
- Select and remove bad digitized head points before automatic coregistration
- Load the MNE -transf.fif: http://neuroimage.usc.edu/forums/showthread.php?2830
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
- Optimize computation interpolation MRI-surface (tess_tri_interp) => spm_mesh_to_grid
BrainSuite:
- Add new labels to all BrainSuite anatomy templates
- Use same colors for left and right for anatomical atlases
- Use for volume coregistration (rigid / non-rigid)
USCBrain: Add default electrodes positions
FEM templates for different ages:
- 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
Scouts:
- Display edges in the middle of the faces instead of the vertices
- Display scouts in a tree: hemisphere, region, subregion
- Sort scouts by region in process options
- Downsample to atlas: allow on timefreq/connect files
- 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
Major bug when importing surfaces for an MRI that was re-oriented manually
Surface>Volume interpolation: Use spm_mesh_to_grid
Bug: Hide scouts in the preview of the grid for volume head models
Geodesic distance calculations:
https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching
Allen Institute gene expression atlases: Import in Brainstorm as source maps and display on cortex

ECOG/SEEG

Electrodes models: Import / export
Contact positions: Import / set / detect
- New option: Align on none|inner|cortex to replace ECOG-mid
- Add history: Save modifications and transformations applied to the channel files (Marcel)
- Project contact positions across subjects or templates (Marcel)
- Add menu to import implantation channel file in imported recordings
SEEG/ECOG: Identify contacts in resected areas / identify ROIs for each contact
SEEG/ECOG: 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)
Display:
- Bad channels: Contacts greyed out instead of ignored (Marcel)
- Display time in H:M:S
- Display curved SEEG electrodes
Export list of contacts with a probability of anatomical regions from various atlases: https://neuroimage.usc.edu/forums/t/seeg-contacts-anatomical-location/14756
Detection CEEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect

Statistics

ANOVA:
- Which functions to use?
- Write panel similar to Process1 and Process2 to allow the
- 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
Quality control before statistics, on condition averages across subjects:
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
Export to R or SPSS for advanced stat

Input / output

Bug import multiple files: use same "time" for all files
BIDS import:
- 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
- Read associated empty room
- Test all the BIDS examples
BIDS Export:
- Add events tsv, channel tsv, EEG, iEEG
XDF import: Use FieldTRip or the EEGLAB plugin, contact Martin Bleichner (Oldenburg)
https://github.com/sccn/xdf/blob/master/xdf_sample.xdf
DICOM converter:
- Add dcm2nii (MRICron)
- Add MRIConvert
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
- The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
- 4D phantom tutorial (JM Badier?)
EEG File formats:
- EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
- 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)
BST-BIN: Add compression to .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
Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284

Distribution & 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
- FieldTrip cortico-muscular coherence tutorial: http://www.fieldtriptoolbox.org/tutorial/coherence
- 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
- BIDS-EEG example datasets
- 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
Workflows FieldTrip: http://www.fieldtriptoolbox.org/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip
Count GitHub clones in the the download stats
Deface the MRIs of all the tutorials

Current bugs

MacOS 10.14.5 (Mojave):
- Toggle buttons do not show their status
- Panel Record: Text is too large for text boxes
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)
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
Canolty maps computation: Fix progress bar

Geeky programming details

Replace all calls to inpolyhd.m with inpolyhedron.m
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.
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)
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)

-  ⇤ ← Revision 273 as of 2016-08-17 21:49:31 → 
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  Editor: FrancoisTadel
  Comment:
+   ← Revision 495 as of 2021-09-19 09:51:51 → ⇥
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  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-== Current topics ==
==== Source modeling ====
 * Implementation of a new unified minimum norm/beamformer framework (work in progress)

==== Documentation ====
 * Standard workflows for different types of data and experiments (work in progress)
 * Cross-validation with MNE and FieldTrip: <<BR>>http://martinos.org/mne/dev/auto_tutorials/plot_brainstorm_auditory.html

==== 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)

<<BR>><<BR>>
-Line 23:
+Line 7:
- * 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
+ * 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
-Line 30:
+Line 19:
- * 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:
  * Pre-load next page of recordings
  * Faster display: Downsample time series before plotting
  * 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
+ * Create heat maps: Maybe with matlab function heatmap?
 * BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)
-Line 44:
+Line 23:
- * Start Brainstorm without Java (-nodesktop)
 * Move code to github
 * Option to increase the size of all the elements of the interface (for high res laptop screens)
 * Allow FieldTrip functions in compiled version
+ * Add a warning when computing a forward model with > 100000 sources (check selection)
 * Snapshot: Save as image / all figures (similar to Movie/all figure)
-Line 51:
+Line 28:
-  * Create a colormap similar to MNE, where extrema are bright
-Line 53:
+Line 29:
- * Open new figures as tab (docked in the Figures window)
-Line 55:
+Line 30:
- * 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...)
-Line 59:
+Line 31:
+ * Contact sheets: Allow explicit list of times in input (+ display as in MNE-Python with TS)
 * Display CTF coils: Show discs instead of squares

 * Progress bar: Add a "Cancel" button
 * Error message: Add a link to report directly the bug on the forum
 * Reorganize menus (Dannie's suggestion): {{attachment:dannie_menus.png||width="382",height="237"}}
-Line 61:
+Line 39:
- * Thresholding and stat tests the connectivity matrices
 * Connectivity on unconstrained sources: how to group the three orientations?
 * 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
+ * Thresholding and stat tests for 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)
 * 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
 * Time-resolved correlation/coherence: Display as time bands
 * Weighted Phase Lag Index (WPLI)
 * Coherence: Average cross-spectra instead of concatenating epochs (to avoid discontinuities)<<BR>>Explore inter-trial approaches (Esther refers to chronux toolbox)
 * Granger: Check for minimum time window (Esther: min around 500-1000 data points)
-Line 86:
+Line 50:
-  * Add p-values
-Line 88:
+Line 51:
-  * Optimize code
-Line 92:
+Line 54:
- * 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
 * 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
-Line 112:
+Line 56:
- * Explore Matlab-Python bridge:<<BR>> https://mail.python.org/pipermail/neuroimaging/2016-June/001001.html
 * Allow processes in Python and Java
+ * Plugin manager:
  * Export all the software environment to a .zip file (brainstorm + all plugins)
 * Generate fully reproducible scripts, including all the interactive/graphical parts:
  * Saving all the interactive operations as process calls
  * Improving the pipeline editor to handle loops over data files or subjects
  * Keeping a better track of the provenance of all the data (History field, and maybe more uniform file names)
 * Add MNE-Python functions:
  * scikit-learn classifiers
  * 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
  * 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
  * Change the graphic renderer from Matlab
-Line 115:
+Line 71:
+  * 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 <<BR>>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
-Line 117:
+Line 85:
-  * ft_volumesegment
  * ft_computeleadfield
  * ft_prepare_heamodel
 * Pipeline editor:<<BR>>
+ * Optimization:
  * 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
-Line 122:
+Line 91:
- * PLS:
  * https://www.rotman-baycrest.on.ca/index.php?section=84
  * meg-pls dot weebly dot com
  * Krishnan 2011: http://www.ncbi.nlm.nih.gov/pubmed/20656037
  * Cheung 2015: http://www.sciencedirect.com/science/article/pii/S1053811915007648
  * McIntosh 2012: http://www.ncbi.nlm.nih.gov/pubmed/22804773
  * McIntosh 2004: http://www.ncbi.nlm.nih.gov/pubmed/15501095
+  * 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)<<BR>>http://www.sciencedirect.com/science/article/pii/S1053811916304232
-Line 131:
+Line 95:
+  * Add Alex's suggestions: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4
  * 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
-Line 134:
+Line 102:
-  * Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)
-Line 136:
+Line 103:
-  * 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
-Line 143:
+Line 105:
+  * 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/
-Line 145:
+Line 110:
-  * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
 * SSS/tSSS: Get implementation from MNE
 * Bandpass:
  * Mark with an event the possible edge effects
  * 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)

  * Use the progress bar

  * Allow display of Avg+StdErr
-Line 163:
+Line 111:
- * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Reports: Click on link reopens exactly the figure
-Line 166:
+Line 112:
-  * Multi-tapers
+  * 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)
-Line 168:
+Line 114:
-  * Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc
-Line 172:
+Line 117:
-  * 2D Layout in spectrum
  * Make much faster and more memory efficient (C functions coded by Matti ?)
-Line 176:
+Line 119:
-  * Pad short epochs with zero values for getting lower frequencies
-Line 178:
+Line 120:
-  * Extend clusters tab to display of TF to overlay TF signals (Svet)
-Line 182:
+Line 123:
- * 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)
+  * 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.
-Line 201:
+Line 128:
- * Add buttons to sort files: by name, by comment, by date
-Line 203:
+Line 129:
- * Navigator: Use F2/F3 to explore the entire database (right now F2 works in a weird way)
-Line 206:
+Line 131:
- * Add notes in the folders (text files, visible as nodes in the tree)

 * Screen captures: save straight to the database
-Line 214:
+Line 135:
- * protocol.mat can be too big: do not store the results links in it (and recreate when loading)
+ * Auto-save:
  * 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

  * Improve auto-save: add tracking file next to protocol.mat, do not save all the time, only when closing app, and reload protocol at stratup if tracking file is still there
-Line 219:
+Line 143:
-  * Alternative, with less limitations: http://research.cs.wisc.edu/htcondor/
-Line 222:
+Line 145:
-  * Documentation: http://fieldtrip.fcdonders.nl/faq#distributed_computing_with_fieldtrip_and_matlab
+  * Documentation: https://www.fieldtriptoolbox.org/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/
-Line 224:
+Line 147:
- * Various initiatives: http://samirdas.github.io/Data_sharing.html#/
-Line 227:
+Line 149:
+ * Unconstrained to flat: Default PCA for stat and connectivity?
 * Sensitivity maps: https://mne.tools/stable/auto_examples/forward/plot_forward_sensitivity_maps.html
 * 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
 * Use eLORETA instead of sLORETA? <<BR>>https://neuroimage.usc.edu/forums/t/compute-eeg-sources-with-sloreta/13425/6
  * "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
 * 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:
  * 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 (algorithm to fit surfaces should be imrpoved)
 * 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
-Line 228:
+Line 164:
-  * Create scout form maximum doesn't work (menu Sources > Max value)
  * Set loose parameter from the interface
+  * Bug when displaying interpolated in MRI viewer
-Line 237:
+Line 172:
- * Dipoles:
  * Project individual dipoles files on a template
  * panel_dipoles: Doesn't work with multiple figures
-Line 241:
+Line 173:
- * 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 250:
+Line 175:
- * 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
-Line 259:
+Line 176:
- * 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
-Line 265:
+Line 177:
- * 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
 * Display spectrum scouts (PSD plots when clicking on "Display scouts" on PSD/full cortex)
-Line 278:
+Line 181:
- * MNI coordinates:
  * Compute with FieldTrip: ft_prepare_sourcemodel (linear and non-linear) => Peter
 * FreeSurfer:
  * Do not save "mid" surface unless specified explicitely with the process version

  * 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)
 * BrainVISA: Add support for MarsAtlas (Guillaume A)
+ * FastSurfer: https://deep-mi.org/research/fastsurfer/
 * '''SimNIBS''': Replace HEADRECO with CHARM (headreco will be removed in SimNIBS 4)

 * Infant templates: Add electrodes positions (at least 10-10)

 * Neurodev MRI database: https://jerlab.sc.edu/projects/neurodevelopmental-mri-database/
 * Multi-Scale Brain Parcellator (Lausanne2008):
  * [[https://github.com/sebastientourbier/multiscalebrainparcellatorhttps://hub.docker.com/r/sebastientourbier/multiscalebrainparcellator|https://github.com/sebastientourbier/multiscalebrainparcellator]]
  * [[https://github.com/sebastientourbier/multiscalebrainparcellatorhttps://hub.docker.com/r/sebastientourbier/multiscalebrainparcellator|https://hub.docker.com/r/sebastientourbier/multiscalebrainparcellator]]
  * https://multiscalebrainparcellator.readthedocs.io/en/latest/

 * Registration:
  * Getting electrode positions from 3D scanners: https://sccn.ucsd.edu/wiki/Get_chanlocs
  * GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
  * Use the same registration for multiple recording sessions that have already re-registered previously (eg. with MaxFilter)
  * When linking multiple EEG recordings including 3D positions, do the registration only once and copy it to all the runs
  * Select and remove bad digitized head points before automatic coregistration
  * Load the MNE -transf.fif: http://neuroimage.usc.edu/forums/showthread.php?2830
 * 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<<BR>>Or use inpolyhedron to get a surface mask and then erode it to get the volume envelope
  * Optimize computation interpolation MRI-surface (tess_tri_interp) => spm_mesh_to_grid
-Line 288:
+Line 207:
-  * Use BrainSuite inner skull for surface generation
+  * Add new labels to all BrainSuite anatomy templates
-Line 290:
+Line 209:
- * Warping: Scale option has to be fixed, it is currently very unstable
+  * Use for volume coregistration (rigid / non-rigid)
 * USCBrain: Add default electrodes positions
 * FEM templates for different ages:
  * 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
-Line 294:
+Line 221:
+  * Sort scouts by region in process options
-Line 295:
+Line 223:
-  * 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
+  * 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
-Line 301:
+Line 226:
- * Smooth surface: Fix little spikes due to irregularities in the mesh
 * Add eyes models to attract eye activity
 * tess_mrimask: Not robust enough to major holes in the brain
+ * Surface>Volume interpolation: Use spm_mesh_to_grid
-Line 305:
+Line 228:
+ * Geodesic distance calculations:<<BR>>https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching
 * Allen Institute gene expression atlases: Import in Brainstorm as source maps and display on cortex
-Line 307:
+Line 232:
+ * Electrodes models: Import / export
-Line 308:
+Line 234:
-  * Import/export electrodes positions in MNI/SCS/MRI coordinates
  * Co-register MRI and CT for electrodes marking in the MRI Viewer<<BR>>=> Mutual information: BrainVISA > Outils > Recalage rigide
  * Automatic segmentation of CT scans: See project of Rodrigo Paz (Marseille/Timone)
  * Import from FreeSurfer/FreeView: Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned
+  * New option: Align on none|inner|cortex to replace ECOG-mid
-Line 313:
+Line 236:
-  * ECOG: How to handle cases where not all the grid contacts are in the channel file? (Marcel)
  * Project contact positions across subjects (Marcel)
+  * Project contact positions across subjects or templates (Marcel)
  * Add menu to import implantation channel file in imported recordings
 * SEEG/ECOG: Identify contacts in resected areas / identify ROIs for each contact
 * SEEG/ECOG: 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)
-Line 316:
+Line 253:
-  * Display SEEG+ECOG contacts at the same time
  * Better way to represent ECOG strips that are not in contact with the skull (new type?)
  * SEEG length: count from the most superficial contact
  * SEEG default view: transparent cortex instead of MRI viewer (Marcel)
  * ECOG: Project on cortex instead of inner skull, just for display (Marcel)
  * Color each strip/grid differently
-Line 323:
+Line 254:
-  * ECOG: Topography display without the 3D coordinates (Marcel)
  * 2DLayout: Should not try to use the actual position of the sensors, just the grids/strips.
-Line 326:
+Line 255:
- * Alternatives to OpenMEEG: SimBio/FieldTrip? Matti Stenroos? NFT/NIST?
 * Prepare tutorial with public dataset (Marcel)
+  * Display curved SEEG electrodes
 * Export list of contacts with a probability of anatomical regions from various atlases: https://neuroimage.usc.edu/forums/t/seeg-contacts-anatomical-location/14756
 * Detection CEEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect
-Line 331:
+Line 261:
-  * Use LENA functions(?)
+  * Which functions to use?
  * Write panel similar to Process1 and Process2 to allow the
-Line 334:
+Line 265:
- * New process to test for Gaussianity using swtest
 * PLS: Partial Least Squares
 * Simulate recordings with specific properties, for stat validation
-Line 340:
+Line 267:
+ * Export to R or SPSS for advanced stat
-Line 342:
+Line 270:
+ * Bug import multiple files: use same "time" for all files
 * BIDS import:
  * 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
  * Read associated empty room
  * Test all the BIDS examples
 * BIDS Export:
  * Add events tsv, channel tsv, EEG, iEEG

 * '''XDF import''': Use FieldTRip or the EEGLAB plugin, contact Martin Bleichner (Oldenburg)<<BR>>https://github.com/sccn/xdf/blob/master/xdf_sample.xdf
 * DICOM converter:
  * Add dcm2nii (MRICron)
  * Add MRIConvert
 * 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
-Line 347:
+Line 292:
-  * References at too far from the head sensors in Marseille 4D system
-Line 350:
+Line 294:
- * Export to EDF
-Line 352:
+Line 295:
-  * Nihon Koden
  * Nicolet EEG: Get from from MNE
-Line 356:
+Line 297:
+  * 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
-Line 357:
+Line 302:
- * 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
 * BIDS-MEG: Automatic loading of BIDS-structured databases
+ * BST-BIN: Add compression to .bst
-Line 363:
+Line 304:
- * 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
+ * SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
 * Get acquisition date from files: Missing for 4D
 * Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284
-Line 367:
+Line 309:
+ * 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: <<BR>>
  * Other public datasets: [[https://github.com/INCF/BIDS-examples/tree/bep008_meg|https://github.com/INCF/BIDS-examples/tree/bep008_meg/]]
  * EEG/research
  * FieldTrip ECOG tutorial: http://www.fieldtriptoolbox.org/tutorial/human_ecog
  * FieldTrip cortico-muscular coherence tutorial: http://www.fieldtriptoolbox.org/tutorial/coherence
  * 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
  * BIDS-EEG example datasets
  * 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 368:
+Line 325:
- * Reference tutorials on Google scholar + ResearchGate
 * Google Analytics: Create template and update the section of the Community page
 * New tutorials:
  * MEG steady-state / high-gamma visual
  * MEG resting state + OMEGA (Guoimar, Jeremy, Beth)
  * Intra-cranial recordings (Marcel)
  * Connectivity: Cortico-muscular coherence
  * Co-register MEG runs (Beth)

 * Missing in page "Cite Brainstorm": Add all the methods used in the software
 * Brainstorm File Exchange: Distribute scripts that users would like to share, but that are too specific to be included in the Brainstorm distribution.  => On GitHub
+ * Count GitHub clones in the the download stats
-Line 382:
+Line 329:
- * Screen capture:
  * Bug on Win8/Win10: doesn't capture the correct part of the screen
  * Window managers with fading effect: captures the top window
+ * MacOS 10.14.5 (Mojave):
  * Toggle buttons do not show their status
  * Panel Record: Text is too large for text boxes
-Line 389:
+Line 336:
-  * (TF) Images are too far apart with EEG 20 channels
-Line 392:
+Line 338:
-  * (time series) Sometimes the lines are not visible
  * (time series) Does not work when DC offset is not removed
-Line 401:
+Line 345:
- * 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
-Line 409:
+Line 348:
- * Hide Java panels instead of deleting them
+ * Replace all calls to inpolyhd.m with inpolyhedron.m
 * 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.
 * 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)
-Line 414:
+Line 355:
- * 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

Recordings

Interface

Connectivity

Processes

Database

Distributed computing

Source modeling

Anatomy

ECOG/SEEG

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Distribution & documentation

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