Differences between revisions 192 and 498 (spanning 306 versions)

What's next

A roadmap to the future developments of Brainstorm.

Contents

Recordings
Interface
Connectivity
Processes
Source modeling
Anatomy
ECOG/SEEG
Statistics
Input / output
Distribution & documentation
Current bugs
Distributed computing
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, 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
- 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.

Source modeling

Unconstrained sources:
- Unconstrained to flat: Default PCA for stat and connectivity?
- Process "Scouts time series": Add PCA option (replace isnorm with radio PCA/Norm)
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
- "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:
- 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
Mixed head models: Bug when displaying interpolated in MRI viewer
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
BEM single sphere: Get implementation from MNE
Volume grid:
- Optimize: 3D display (better than 9x9 cubes)
- Optimize: vol_dilate (with 26 neighbors)
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)
Electrode postions:
- GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
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
BrainSuite:
- Use same colors for left and right for anatomical atlases
- Use for volume coregistration (rigid / non-rigid)
- USCBrain: Add default electrodes positions
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
- Neurodev database: https://jerlab.sc.edu/projects/neurodevelopmental-mri-database/
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
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

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

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/

Geeky programming details

Replace all calls to inpolyhd.m with inpolyhedron.m (10x faster)
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 192 as of 2016-02-02 16:37:31 → 
  Size: 21035
  Editor: FrancoisTadel
  Comment:
+   ← Revision 498 as of 2021-09-19 11:59:46 → ⇥
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  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
-== Current topics ==
==== Source modeling ====
 * Implementation of a new unified minimum norm/beamformer framework (work in progress)

==== Statistics ====
 * Implementation of new parametric and non-parametric tests (work in progress)

==== Documentation ====
 * Standard workflows for different types of data and experiments (work in progress)

==== Functional connectivity ====
 * Significance thresholding of the connectivity matrices (not started)

==== Computation ====
 * Removing the dependence to the Java interface to run in headless mode (not started)
 * Interacting directly with distributed computing systems  (not started)

<<BR>><<BR>>
+<<TableOfContents(2,2)>>
-Line 24:
+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 31:
+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)
 * RAW file viewer:
  * Pre-load next page of recordings
  * Events: Change the category of a selected event easily, instead of deleting/marking new
  * Events: advanced process for recombining.
  * Example:  http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
 * Bad channels specified at the program level (for sites that have permanent bad channels: AS)
 * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time]
  * Can be done with Matrix > View as image: extract cluster, concatenate for all trials
 * Filtering:
  * Use short FIR filters instead of IIR for bandpass, to limit the ringing (bad for Hilbert as well)
  * Or allow the users to edit the LowStop parameter in bst_bandpass.

 * Show easily recordings maximum/values in the file viewer
+ * Create heat maps: Maybe with matlab function heatmap?
 * BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)
-Line 51:
+Line 23:
- * Start Brainstorm without Java (-nodesktop)
 * Generalize the user of the units (field .Units): Rewrite processes to save the units correctly
+ * 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
-Line 54:
+Line 28:
-  * Manage multiple custom colormaps
-Line 56:
+Line 29:
-  * Create a colormap similar to MNE, where extrema are bright
-Line 58:
+Line 30:
- * Open new figures as tab (docked in the Figures window)
-Line 60:
+Line 31:
- * 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...)
+ * 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): {{attachment:dannie_menus.png||width="382",height="237"}}
-Line 65:
+Line 40:
- * Thresholding the connectivity matrices
 * t-tests on connectivity measures
 * Check why our Hilbert implementation has huge edge effects
 * Connectivity on unconstrained sources: how to group the three orientations?
 * Connectivity based on band limited power (Sylvain):
  * Compute Hilbert/Bandpass + correlation of the envelopes
  * Bandpass envelopes before computing correlations?
  * Compute Hilbert(sensors) and then project to source space?
 * Multi-tapers?
 * Graph view:
  * Does not display negative values correctly (correlation or difference of coherence)
  * Re-write using pure Matlab code and smoothed graphics
  * Fixed scales for intensity sliders
  * Text bigger
  * Too much data in appdata
  * Fixed scales for intensity sliders
  * Add "=" shortcut for having graphs with similar configurations
  * Disable zoom in one region (serious bugs)
  * NxN on sensors: does not place the sensors correctly in space
 * Coherence:
  * Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
 * Granger:
  * Crashes sometimes: improve stability
  * Re-write and optimize code
  * Add progress bar
+ * 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 91:
+Line 51:
-  * Add p-values
-Line 93:
+Line 52:
-  * Optimize code
-Line 96:
+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)
 * 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
+  * Add warning when running of short windows (because of filters)
-Line 113:
+Line 57:
- * Edit FieldTrip path in the user preferences
 * Optimize pipeline editor speed: Opening the window and the showing menu "Add process" are slow
+ * 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, 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
 * 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 <<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
  * 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)<<BR>>http://www.sciencedirect.com/science/article/pii/S1053811916304232
-Line 116:
+Line 96:
+  * 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 117:
+Line 101:
+  * Export IC time series (and then compute their spectrum): solves the problem above
-Line 118:
+Line 103:
-  * Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)
-Line 120:
+Line 104:
-  * 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 126:
+Line 105:
- * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Allow processes in Python and Java
+  * 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/
-Line 130:
+Line 111:
-  * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
 * Bandpass:
  * Offer option: bst_bandpass_fft / bst_bandpass_filter
  * Rewrite without the forced low-pass filter at Fs/3
  * Show warning when using inappropriate high-pass filter (precision too high)
  * Use FIR filter
 * Spectral flattening (John):
  * ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis

 * PSD:
  * Rewrite to have the same input as coherence (frequency resolution instead of window length)

  * Allow running on source files attached to continuous files (needs a lot of rewriting)
-Line 144:
+Line 112:
- * Band-limited power envelope
 * Reports:
  * Save as HTML / PDF
  * Do not display the intermediate files
 * Pipeline editor:
  * Add loops over subjects/conditions/trial groups
  * Allow the to stack to Process2 together (file selection + test): Add a number of outputs for each process2 (1 or 2), to know if they can be stacked with another process2
-Line 152:
+Line 113:
-  * Induced calculation: Avg(Power(TF(trials - Avg(Trials)))): <<BR>>Add option "Remove evoked response from each trial"
  * Standardize using: diff before calculation + cumsum (checkbox "flatten data")
  * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  * Display logs as negative
  * Difference of power displayed in log: problems (Soheila)
  * 2D Layout in spectrum
  * Make much faster and more memory efficient (C functions coded by Matti ?)
  * TF scouts: should display average of TF maps
  * Impossible to keep complex values for unconstrained sources
  * Pad short epochs with zero values for getting lower frequencies
+  * 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
-Line 163:
+Line 116:
-  * 3D figures: Colormaps with "log" option doesn't work
  * Extend clusters tab to display of TF to overlay TF signals (Svet)
  * TF on scouts: Add progress bar when extracting all the scouts time series (can be long)
 * Artifact detection:
  * Artifact rejection like SPM: if bad in 20%, bad everywhere
  * Test difference between adjacent samples
  * Allow the detection on differences of signals (bipolar montages)
 * Co-registration of MEG runs:
  * SSP: Group projectors coming from different files
  * Finish validation of the method
  * Apply to continuous recordings for correcting head movements
 * Resample continuous files
 * Other processes:
  * Moving average
  * Max
  * Median
  * Significance test (Dimitrios, Leo)
  * Spatial smoothing: check / document parameters
 * Contact sheets & movies: use average of time windows instead of single instants, for each picture.
 * Optical flow
 * Simulation:
  * Fix units in simulation processes => no *1e-9 in "simulate recordings"
  * Use "add noise" process from Hui-Ling (in Work/Dev/Divers)
 * Use field process field "Group" to separate Input/Processing/Output options
 * Use new Matlab functions: movmean, movsum, movmedian, movmax, movmin, movvar, movstd

== Database ==
 * Sort files by comment
 * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
 * Matrix files:
  * Group matrix files => allow to process matrix files by trial types
  * Allow to be dependent from other files

 * Add notes in the folders (text files, visible as nodes in the tree)

 * Screen captures: save straight to the database

 * Rename multiple files

 * Default headmodel lost when reloaded: Keep selection on the hard drive (in brainstormstudy.mat)

== Distributed computing ==
 * Options from FieldTrip:
  * Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer
  * Alternative, with less limitations: http://research.cs.wisc.edu/htcondor/
  * Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine
  * Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub
  * Documentation: http://fieldtrip.fcdonders.nl/faq#distributed_computing_with_fieldtrip_and_matlab
 * PSOM: http://psom.simexp-lab.org/
+  * 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.
-Line 214:
+Line 122:
- * Mixed head models:
  * Project to templates (scouts or source maps)
  * Create scout form maximum doesn't work (menu Sources > Max value)
  * Display in MRI doesn't work
  * Smooth display: do not smooth subcortical structures
  * Export as .nii volume: doesn't work
+ * Unconstrained sources:
  * Unconstrained to flat: Default PCA for stat and connectivity?
  * Process "Scouts time series": Add PCA option (replace isnorm with radio PCA/Norm)

 * 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
  * "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
-Line 221:
+Line 136:
+  * Project individual dipoles files on a template
-Line 222:
+Line 138:
-  * Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates
 * Panel Get coordinates: Add button "find maximum"
 * Stenroos 2014 paper: Include the following methods
  * Inner and outer skull surfaces generator from FieldTrip (needs SPM)
  * Nolte corrected-sphere model (good model re:Alex)
  * Fast BEM models
 * Visualize Beamformer results:
  * Read CTF SAM .svl
  * Display as layers in the MRI viewer
 * Unconstrained sources:
  * Stat and connectivity: what to do? (re-send email John+Sylvain)
 * Overlapping spheres: improve the estimation of the spheres for the frontal lobes
+ * Project sources: Very poor algorithm to project sub-cortical regions and cerebellum
 * Mixed head models: Bug when displaying interpolated in MRI viewer
 * 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
 * BEM single sphere: Get implementation from MNE
-Line 235:
+Line 146:
-  * Test volume sources with all the subsequent processes (timefreq, stat...)
-Line 238:
+Line 148:
- * Magnetic extrapolation: Do the same thing with EEG
 * Noise covariance matrix:
  * Display with figure_image()
  * Storage of multiple noise covariance matrices (just like the head models)
  * Always save as full, then at inversion time, we can decide between full, heteroskedastic (diagonal) or homoskedastic (i.i.d, scalar)
  * Problem of having inividual trials + averages in the condition => Display warning or not?
  * Save nAvg in noisecov file, to make it easier to scale to other recordings
  * When deploying to other conditions: Apply destination SSP (NoiseCov = SSP.NoiseCov.SSP' )
 * Sources on surface: Display peak regions over time (time = color) => A.Gramfort
 * Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise)
 * Calculate ImagingKernel * Gain for a scout
 * EEG Source modeling: Manage references and bipolar montages properly (maybe not necessary)
 * MEG source modeling: Do reconstruction only for a subset of sensors for estimating dipoles?
 * Processes compute head model and sources: Additional option to set the file comment
 * Beamformers from FieldTrip (LCMV, SAM)
 * Time-frequency beamformers:
  * Band-pass everything in different frequency bands + Source estimation + TF
  * Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF
 * Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
 * BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
 * Hui-Ling beamformers:
  * More explanations about what is in NAI and Spatial filters
  * Explain that is this is better to study effects extended in time (Ntime > Nsensors)
  * Group LCMV+MCB
  * Condition LEFT median nerve: very bad results
 * Menu Sources > Simulate recordings:
  * Do not close the 3D figures after generating a new file
  * Add a process equivalent to this menu
+ * Add eyes models to attract eye activity
 * Display spectrum scouts (PSD plots when clicking on "Display scouts" on PSD/full cortex)
-Line 268:
+Line 152:
- * MNI coordinates: Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256)
 * Project all sub-cortical structures to default anatomy (check code from Denis S)
 * Add cerebellum to default model generated with "Import FS anatomy"
 * Import MRIs with different resolutions: re-interpolate automatically
 * Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
 * Warping: Scale option has to be fixed, it is currently very unstable
+ * FastSurfer: https://deep-mi.org/research/fastsurfer/
 * '''SimNIBS''': Replace HEADRECO with CHARM (headreco will be removed in SimNIBS 4)

 * Electrode postions:
  * GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation

 * 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
  * Surface>Volume interpolation: Use '''spm_mesh_to_grid''' instead of tess_tri_interp
 * BrainSuite:
  * Use same colors for left and right for anatomical atlases
  * Use for volume coregistration (rigid / non-rigid)
  * USCBrain: Add default electrodes positions
 * 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
  * Neurodev database: https://jerlab.sc.edu/projects/neurodevelopmental-mri-database/
-Line 276:
+Line 179:
-  * Display scouts in a tree: hemisphere, region, subregion
  * Downsample to atlas: allow on timefreq/connect files
  * Sort scouts by region in process options
 * Menu head model > Copy to other conditions/subjects (check if applicable first)
 * Generate mixed density surfaces
 * Optimize computation interpolation MRI-surface (tess_tri_interp)
 * Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
 * Major bug when importing surfaces for an MRI that was re-oriented manually
 * Smooth surface: Fix little spikes to irregularities in the mesh
 * Add eyes models to attract eye activity
+  * 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
 * 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
-Line 288:
+Line 185:
- * Co-register MRI and CT for electrodes marking in the MRI Viewer
 * Import/export electrodes positions in MNI/SCS/MRI coordinates
 * Display SEEG+ECOG contacts at the same time
 * Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned
+ * 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
-Line 294:
+Line 213:
- * t-test/diff_mean between trial groups: better file comments
 * ANOVA: Use LENA functions(?)
+ * ANOVA:
  * Which functions to use?
  * Write panel similar to Process1 and Process2 to allow the
-Line 298:
+Line 218:
- * Problem t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo
  * Waiting for test from Dimitrios
  * Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test
  * http://fr.wikipedia.org/wiki/Test_de_Shapiro-Wilk
  * http://stats.stackexchange.com/questions/362/what-is-the-difference-between-the-shapiro-wilk-test-of-normality-and-the-kolmog
  * http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html
  * http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html
  * http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab
 * Stat FieldTrip: impossible to do Abs(Mean(Sources)) => Is it a problem?
 * Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter
 * PLS: Partial Least Squares
 * In Stat tab: Correction by temporal extension (display only if effect longer than a given input in ms)
+ * 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
 * Export to R or SPSS for advanced stat
-Line 312:
+Line 223:
- * FieldTrip integration:
  * Import/Export continuous recordings and non-averaged trials.
  * Export trials with a trial definition: http://neuroimage.usc.edu/forums/showthread.php?2213
+ * 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
 * 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?)
-Line 318:
+Line 250:
+  * 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 319:
+Line 255:
- * EEGLAB import:
  * Support for binary AND epoched files (now it's one or the other)
  * Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
 * BST-BIN: Add compression
+ * BST-BIN: Add compression to .bst
-Line 324:
+Line 257:
- * 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 328:
+Line 262:
- * Reference tutorials on Google scholar + ResearchGate
 * Cleaning threads on the forum
 * Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
 * Finish existing tutorials:
  * EEG/Epilepsy: Rewrite scripts + update contents (with Geneva2015 walkthrough)
  * Dipoles
  * Auditory: Finish scripts
  * Group MEM/Epilepsy + Epilepsy tutorials
 * New tutorials:
  * MEG connectome
  * Scrambled faces (SPM/MNE-Python)
  * Coherence (cortico-muscular ?)
  * Intra-cranial recordings
  * Co-register MEG runs (Beth)
 * Missing in the introduction tutorials:
  * Volume scouts
  * Sources: Model evaluation (by simulating recordings)
  * Time-frequency: Description of "log freq scale" option
  * Modify a structure manually: Export to Matlab/Import from Matlab
  * File manipulation: file_short, file_fullpath, in_bst_*...
  * Description of all fields in MRI and surfaces
 * Script tutorials: ask what folder contains the tutorial datasets
 * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
 * Missing in page "Cite Brainstorm": Add all the methods used in the software
+ * 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
 * 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
-Line 354:
+Line 282:
- * 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 361:
+Line 289:
-  * (TF) Images are too far apart with EEG 20 channels
  * (time series) Sometimes the lines are not visible
  * (time series) Does not work when DC offset is not removed
+  * (TF) Units are weird with % values
  * (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling
-Line 371:
+Line 298:
- * Matlab bugs:
  * Interface looks small on screens with very high resolutions: Reduce the resolution
  * Out of memory errors on Win 32bits (restart Matlab)
  * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
 * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG
 * in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
 * Edit scout in MRI: small modifications cause huge increase of the scout size
-Line 380:
+Line 300:
+== 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/
-Line 381:
+Line 309:
- * Hide Java panels instead of deleting them
+ * Replace all calls to inpolyhd.m with inpolyhedron.m (10x faster)
 * 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"
-Line 385:
+Line 316:
- * Optimize bst_get:
  * Now study and subject have necessarily the same folder name
  * Replace big switch with separate functions
 * Progress bar:
  * Add different levels (to handle sub-processes)
  * Make work correctly with RAW on resting tutorial
  * Uniformize calls in bst_process/Run
  * Add a "Cancel" button
 * Fix all the 'todo' blocks in the code
 * Replace handle "0" with bst_get('groot')
 * At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame)
 * Error message: Add a link to report directly the bug on the forum
 * Optimize MRI viewer with patch() instead of image()

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