Differences between revisions 159 and 579 (spanning 420 versions)

What's next

A roadmap to the future developments of Brainstorm.

Contents

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

Recordings

Review signals in time-frequency space
Events processes: Select events names from a list instead of having to type them
Display CTF coils: Show discs instead of squares
Sleep scoring wish list (Emily C):
- Configurable horizontal lines (for helping detecting visually some thresholds)
- Mouse ruler: Measure 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 (Low priority) :
- Consider to change to a format that is faster to read
- Add parameter to make the visual downsampling more or less aggressive
- Keep the filter specifications in memory instead of recomputing for every page
  (Nice to have)
BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)
Simulations: https://github.com/lrkrol/SEREEGA(Low priority)

ECOG/SEEG

https://www.sciencedirect.com/science/article/pii/S1053811922005559
Display (high-priority)(Part SEEG grant):
- Group display: Overlay multiple channel files in the same figure, coloring contacts by subject/ROI/Cluster/Electrode name
  - https://neuroimage.usc.edu/forums/t/37617
  - iEEG tab must be read-only when multiple files (hide configuration controls)
- Bad channels: Contacts greyed out instead of ignored (Marcel H, Germany)
  (To diff between band and not-recorded) > Rendering of SEEG electrodes: Full surface modelling with surface mesh (see Lead-DBS models + code that generates them?)
- Display time in H:M:S instead of S > If there is t0 in H:M:S instead of S > As an option in Display configuration button>x-axis
- view_leadfield_sensitivity: Add closing surfaces at cortex limits
Create clusters from anatomical labels (Anne So) :
- 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> As a process to select recordings, then Scouts from Volumen Atlas, Create cluster in channel file, then Extract time series.
- Group analysis: extract clusters across subjects, display or average signals (see MIA) (Anne So)
Spike detection (Need to check for current toolboxes from scratch)(contact Nicolas R)(Mosher J)(iEEG BIDS):
- https://iopscience.iop.org/article/10.1088/1741-2552/ac9259/pdf
Automatic segmentation of CT:
- LeGUI: https://github.com/Rolston-Lab/LeGUI/tree/main/LeGUI<<BR>>https://neuroimage.usc.edu/forums/t/automatic-localization-of-seeg-electrodes/36302/7
- GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
- SEEG DEETO Arnulfo 2015: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0511-6
  - Used routinely at Niguarda Hospital + other hospitals worldwide, reliable tool.
  - To be used with SEEG-assistant/3DSlicer: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1545-8
- ECOG Centracchio 2021: https://link.springer.com/content/pdf/10.1007/s11548-021-02325-0.pdf
  - Classifier on thresholded CT: https://github.com/Jcentracchio/Automated-localization-of-ECoG-electrodes-in-CT-volumes
- SEEG Granados 2018 (no code shared): https://link.springer.com/content/pdf/10.1007/s11548-018-1740-8.pdf
ECOG:
- Project and display contacts on cortex surface should consider the rigidity of the grids: Contacts cannot rotate, and distance between contacts should remain constant across runs
- Method for contacts projection: https://pdfs.semanticscholar.org/f10d/6b899d851f3c4b115404298d7b997cf1d5ab.pdf
- ECOG: Brain shift: When creating contact positions on a post-implantation image, the brain shift should be taken into account for creating images of the ECOG contacts on the pre-op brain => iELVis (http://ielvis.pbworks.com/w/page/116347253/FrontPage)
  Normalization MNI? solutions with FieldTrip?
Display CT images: Better brightness/contrast adjustment: https://neuroimage.usc.edu/forums/t/automatic-localization-of-seeg-electrodes/36302/8 Range of values is way diff than ones from MRI. Current color maps are not suitable for CT, need to be improved.Together with processing of CT to get electrode positions.
Detection CCEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect https://f-tract.eu/software/imagin/

Pre-processing

process_detectbad:
- Allow on raw files (for bad channels only)
- Add detection on derivative of the signal (see EEGLAB)
- Document in tutorial Bad channels
- PREP pipeline / EEGLAB (Bigdely-Shamlo 2015)
Improve bad channel/trial detection:
- ft_artifact_threshold and ft_rejectartifact
- MNE-Python
- EEGLAB
Integrate with EYE-EEG (Olaf Dimigen)
- Reproduce tutorial: https://www.eyetracking-eeg.org/tutorial.html
- Create EYE-EEG plugin + processes (Raphael Lambert)
- Process: Detect sacades (extended events) + fixations
- Improved ICA
- Eye-movement related potentials
Add note when rejecting trials: https://neuroimage.usc.edu/forums/t/33686
ICA:
- Automatic classification: ICLabel: https://neuroimage.usc.edu/forums/t/automatic-eeg-ic-ica-classification-for-brainstorm/33785
- Exploration: Add window with spectral decomposition (useful for muscle artifacts)
- Export IC time series (and then compute their spectrum): solves the problem above
- Import ICA matrices available in EEGLAB .set files
- 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
File format:
- Add support to read GDF file format

https://github.com/donnchadh/biosig/blob/master/biosig/t200_FileAccess/sload.m

Reproducibility toolbox

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

Interface

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

Database

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

Connectivity

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

Processes

Add MNE-Python functions:
- scikit-learn classifiers
- BEM single layer (John wants to test it)
- ICA: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4
- https://neuroimage.usc.edu/forums/t/best-way-to-export-to-mne-python/12704/3
- Reproduce other tutorials / examples
- Point-spread functions (PSFs) and cross-talk functions: https://mne.tools/stable/auto_examples/inverse/plot_psf_ctf_vertices.html#sphx-glr-auto-examples-inverse-plot-psf-ctf-vertices-py
- Spatial resolution metrics in source space:
  https://mne.tools/stable/auto_examples/inverse/plot_resolution_metrics.html#sphx-glr-auto-examples-inverse-plot-resolution-metrics-py
- Change the graphic renderer from Matlab
Chronux toolbox : http://chronux.org/
Add FieldTrip functions:
- ft_sourceanalysis:
  - Check noise covariance
  - Check all the options of all the methods
  - Single trial reconstructions + noise covariance?
  - Filters?? http://www.fieldtriptoolbox.org/example/common_filters_in_beamforming
  - Beamformers: Save ftSource.avg.mom
    http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo
  - http://www.natmeg.se/ft_beamformer/beamformer.html
  - http://www.fieldtriptoolbox.org/tutorial/beamformingextended
  - Baseline? Two inputs?
- ft_prepare_heamodel: Add support from BEM surfaces from the Brainstorm database
- Freqanalysis: ITC
- ft_volumereslice: http://www.fieldtriptoolbox.org/faq/how_change_mri_orientation_size_fov
- ft_freqanalysis
- ft_combineplanar
Optimization:
- Test speed for writing files:
  https://undocumentedmatlab.com/articles/improving-fwrite-performance
- Use CUDA for speeding up some operations (filtering, wavelets, etc)
- Use Matlab Coder to optimize: Wavelets, bandpass filter, sinusoid removal
Pipeline editor:
- Bug: After "convert to continuous", the time of the following processes should change
- Add loops over subjects/conditions/trial groups
- Events: Allow selection from a drop-down list (similar to option "channelname" in panel_process_selection)
ITC: Inter-trial coherence (see MNE reports for group tutorial)
http://www.sciencedirect.com/science/article/pii/S1053811916304232
Remove line noise: http://www.nitrc.org/projects/cleanline
Time-frequency:
- Optimization: bst_timefreq (around l.136), remove evoked in source space: Average should be computed in sensor space instead of source space (requested by Dimitrios)
- Short-time Fourier transform: http://www.mikexcohen.com/lectures.html
- Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead.
- When normalizing with baseline: Propagate with the edge effects marked in TFmask
- Allow running TF on montages
- Review continuous files in time-frequency space (for epilepsy)
- Bug when computing TF on constrained and unconstrained scouts at the same time (in mixed head models for instance): uses only the constrained information and doesn't sum the 3 orientations for the unconstrained regions.

Anatomy

Import SimNIBS4: Use final_tissues_LUT.txt instead of fixed list of tissues: https://neuroimage.usc.edu/forums/t/removing-a-lesioned-area/38414/20
Simple-brain-plot: https://github.com/dutchconnectomelab/Simple-Brain-Plot
MNI normalization: More options:
- DARTEL / SHOOT
- BrainSuite (wait for Anand)
- Import from SimNIBS (Conform2MNI_nonl.nii.gz, MNI2Conform_nonl.nii.gz)
MRI Viewer:
- Adjust CT contrast better: https://neuroimage.usc.edu/forums/t/automatic-localization-of-seeg-electrodes/36302/10
- Pan in zoomed view (shift + click + move?)
- Zoom in/out with mouse (shift + scroll?)
- Ruler tool to measure distances
- Display scouts as additional volumes
- Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
  Or use inpolyhedron to get a surface mask and then erode it to get the volume envelope
- Surface>Volume interpolation: Use spm_mesh_to_grid instead of tess_tri_interp
Defacing:
- https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html
- Removing MNI face mask using MNI coordinates
Atlas switch in 3D MRI figures
Bug import anatomy: Requested nVert > high-resolution cortex surface: Creates an empty cortex_0V
BrainSuite:
- Use same colors for left and right for anatomical atlases
- Use for volume coregistration (rigid / non-rigid)
- USCBrain: Add default electrodes positions
- Remove BrainSuite1 when not needed anymore
Brain2mesh: Add import of 10-10 positions
Templates for different ages:
Scouts:
- Display edges in the middle of the faces instead of the vertices
Parcellating volume grids: scikit-learn.cluster.Ward
Geodesic distance calculations:
https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching
Improving the registration between EEG and anatomy templates:
- Warping: Improve the basic alignment of the digitized electrodes on the templat, possibly with Cz and other anatomical landmarks
- EEG template positions: rework using a standardized Cz position (+ other landmarks)

Forward modeling

DUNEuro/FEM:
- Add lesion mask to SimNIBS: https://simnibs.github.io/simnibs/build/html/documentation/command_line/add_tissues_to_upsampled.html#add-tissues-to-upsampled-doc
- GeomtryAdapted: Buggy?
- Display differences between leadfields: amplitude of difference (right-click > Compare)
- Display sensitivity on FEM surface
OpenMEEG: Detect bad results + exclude from leadfield
BEM single sphere: Get implementation from MNE
Add eyes models to attract eye activity

Source modeling

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

Statistics

Stat on unconstrained sources?
Stat/time series: Hide lines going down to zero (Dimitrios: https://neuroimage.usc.edu/forums/t/common-source-activation-across-subjects-and-conditions/1152/21)
Cluster stat: Add frequency selection option
ANOVA:
- Write panel similar to Process1 and Process2
- Output = 1 file per effect, all grouped in a node "ANOVA"
- Display several ANOVA maps (from several files) on one single figure, using a "graphic accumulator", towards which one can send any type of graphic object
Multivariate stim-response analysis: https://github.com/mickcrosse/mTRF-Toolbox

Input / output

BIDS import:
- Add option to process to specify the protocol name
- Full support for iEEG and EEG
- Disable logging of sub-processes (reloading the previous report should only show process_import_bids)
- Read real fiducials (OMEGA) / transformation matrices:
- Use BIDS-Matlab?
Test datasets:
- See list of test datasets in process_import_bids.m
- ds004085 / ds004473: Check response epoch + BUG with coordinate interpretation
BIDS export:
- EEG, iEEG: Add events.tsv, channel.tsv, electrodes.tsv
- Anatomy: Add t1w.json (including fiducials)
- Use BIDS-Matlab?
EDF+ reader: Add resampling of channels with different sampling rates
Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284
DICOM converter:
- Add dcm2nii (MRICron)
- Add MRIConvert
SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
EEG File formats:
- XLTEK: https://github.com/danielmhanover/OpenXLT
- Persyst .lay: https://github.com/ieeg-portal/Persyst-Reader
- Nervus .eeg: https://github.com/ieeg-portal/Nervus-Reader
- Biopac .acq: https://github.com/ieeg-portal/Biopac-Reader
- BCI2000 Input (via EEGLAB plugin)
4D file format:
- Use reader from MNE-Python: mne.io.read_raw_kit (skip Yokogawa slow library)
- Reference gradiometers: Keep the orientation of the first or second coil?
- Reference gradiometers: Add the sensor definition from coil_def.dat
- Validate with phantom recordings that noise compensation is properly taken into account
- The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
- 4D phantom tutorial (JM Badier?)
BST-BIN: Add compression to .bst
MINC MRI: Add support for "voxel to world" transformation (vox2ras) similarly to .nii

Distribution

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

Documentation

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

Current bugs

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

Distributed computing

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

Geeky programming details

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

-  ⇤ ← Revision 159 as of 2015-05-06 22:32:57 → 
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+   ← Revision 579 as of 2023-09-13 19:42:51 → ⇥
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-== Current topics ==
==== Documentation ====
 * Merging the 12+3 introduction tutorials to illustrate better the latest developments

==== Source modeling ====
 * Implementation of a new unified minimum norm/beamformer framework

==== Functional connectivity ====
 * Significance thresholding of the connectivity matrices

==== Computation ====
 * Removing the dependence to the Java interface to run in headless mode
 * Interacting directly with distributed computing systems

==== Compatibility ====
 * Reading and writing FieldTrip structures
 * Calling FieldTrip functions from the pipeline

<<BR>><<BR>>
+<<TableOfContents(2,2)>>
-Line 25:
+Line 7:
- * Nicer 2D topographies, standardized (using FieldTrip .lay files?)
 * 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: 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
  * Or allow the users to edit the LowStop parameter in bst_bandpass.

 * Show easily recordings maximum/values in the file viewer
+ * Review signals in time-frequency space
 * Events processes: Select events names from a list instead of having to type them
 * Display CTF coils: Show discs instead of squares
 * Sleep scoring wish list (Emily C):
  * Configurable horizontal lines (for helping detecting visually some thresholds)
  * Mouse ruler: Measure 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 (Low priority) :<<BR>>

  * Consider to change to a format that is faster to read
  * Add parameter to make the visual downsampling more or less aggressive
  *
  Keep the filter specifications in memory instead of recomputing for every page<<BR>>(Nice to have)


 *
 BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)

 *
 Simulations: https://github.com/lrkrol/SEREEGA(Low priority)


== ECOG/SEEG ==
 *
 https://www.sciencedirect.com/science/article/pii/S1053811922005559

 * Display (high-priority)(Part SEEG grant):
  * Group display: Overlay multiple channel files in the same figure, coloring contacts by subject/ROI/Cluster/Electrode name
   *
   https://neuroimage.usc.edu/forums/t/37617

   * iEEG tab must be read-only when multiple files (hide configuration controls)

  *
  Bad channels: Contacts greyed out instead of ignored (Marcel H, Germany)<<BR>>(To diff between band and not-recorded) > Rendering of SEEG electrodes: Full surface modelling with surface mesh (see Lead-DBS models + code that generates them?)

  *
  Display time in H:M:S instead of S > If there is t0 in H:M:S  instead of S > As an option in Display configuration button>x-axis

  * view_leadfield_sensitivity: Add closing surfaces at cortex limits

 * Create clusters from anatomical labels (Anne So) :
  *
  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> As a process to select recordings, then Scouts from Volumen Atlas, Create cluster in channel file, then Extract time series.

  * Group analysis: extract clusters across subjects, display or average signals (see MIA) (Anne So)

 * Spike detection (Need to check for current toolboxes from scratch)(contact Nicolas R)(Mosher J)(iEEG BIDS):
  *
  https://iopscience.iop.org/article/10.1088/1741-2552/ac9259/pdf


 * Automatic segmentation of CT:
  *
  LeGUI: https://github.com/Rolston-Lab/LeGUI/tree/main/LeGUI<<BR>>https://neuroimage.usc.edu/forums/t/automatic-localization-of-seeg-electrodes/36302/7

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

  *
  SEEG DEETO Arnulfo 2015: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0511-6

   * Used routinely at Niguarda Hospital + other hospitals worldwide, reliable tool.
   *
   To be used with SEEG-assistant/3DSlicer: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1545-8


  *
  ECOG Centracchio 2021: https://link.springer.com/content/pdf/10.1007/s11548-021-02325-0.pdf

   *
   Classifier on thresholded CT: https://github.com/Jcentracchio/Automated-localization-of-ECoG-electrodes-in-CT-volumes


  *
  SEEG Granados 2018 (no code shared): https://link.springer.com/content/pdf/10.1007/s11548-018-1740-8.pdf


 * ECOG:
  * Project  and display contacts on cortex surface should consider the rigidity of  the grids: Contacts cannot rotate, and distance between contacts should  remain constant across runs
  *
  Method for contacts projection: https://pdfs.semanticscholar.org/f10d/6b899d851f3c4b115404298d7b997cf1d5ab.pdf

  *
  ECOG:  Brain shift: When creating contact positions on a post-implantation  image, the brain shift should be taken into account for creating images  of the ECOG contacts on the pre-op brain => iELVis (http://ielvis.pbworks.com/w/page/116347253/FrontPage) <<BR>>Normalization MNI? solutions with FieldTrip?


 *
 Display CT images: Better brightness/contrast adjustment: https://neuroimage.usc.edu/forums/t/automatic-localization-of-seeg-electrodes/36302/8 Range of values is way diff than ones from MRI. Current color maps are not suitable for CT, need to be improved.Together with processing of CT to get electrode positions.

 *
 Detection CCEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect https://f-tract.eu/software/imagin/


== Pre-processing ==
 * process_detectbad:
  * Allow on raw files (for bad channels only)
  * Add detection on derivative of the signal (see EEGLAB)
  * Document in tutorial Bad channels
  * PREP pipeline / EEGLAB (Bigdely-Shamlo 2015)

 * Improve bad channel/trial detection:
  * ft_artifact_threshold and ft_rejectartifact
  * MNE-Python
  * EEGLAB

 * Integrate with EYE-EEG (Olaf Dimigen)
  *
  Reproduce tutorial: https://www.eyetracking-eeg.org/tutorial.html

  * Create EYE-EEG plugin + processes  (Raphael Lambert)
  * Process: Detect sacades (extended events) + fixations
  * Improved ICA
  * Eye-movement related potentials

 *
 Add note when rejecting trials: https://neuroimage.usc.edu/forums/t/33686


 *
 ICA: <<BR>>

  *
  Automatic classification: ICLabel: https://neuroimage.usc.edu/forums/t/automatic-eeg-ic-ica-classification-for-brainstorm/33785

  * Exploration: Add window with spectral decomposition (useful for muscle artifacts)
  * Export IC time series (and then compute their spectrum): solves the problem above
  * Import ICA matrices available in EEGLAB .set files
  *
  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


 * File format:
  * Add support to read GDF file format
https://github.com/donnchadh/biosig/blob/master/biosig/t200_FileAccess/sload.m
 * <<BR>>
  *


== Reproducibility toolbox ==
 * Generate fully reproducible scripts, including all the interactive/graphical parts
 * Record all GUI actions as script calls
 * Import window: Add button to create the corresponding processing pipeline (to generate script or to edit additional options)
 * Adding the list of plugins to the reports (optionnal or foldable)
 * Better provenance: History fields, uniform file names...
 * Improving the pipeline editor to handle loops over data files or subjects
-Line 45:
+Line 171:
- * Colormaps:
  * Manage multiple custom colormaps
  * Allow brightness/contrast manipulations on the custom colormaps
  * Create a colormap similar to MNE, where extrema are bright
  * Global colormap max: Should get the maximum across all the open files
 * Open new figures as tab (docked in the Figures window)
 * Copy figures to clipboard (with the screencapture function)
 * Removing all the CTRL and SHIFT in the keyboard shortcuts
 * Display warning before opening files that are too big
+ *
 Add a warning when computing a forward model with > 100000 sources (check selection)

 * Colormaps: Global colormap max: Should get the maximum across all the open files

 * Snapshot:
  * Save as image / all figures (similar to Movie/all figure)
  * Copy figures to clipboard (with the screencapture function)

 *
 Contact sheets & movies: use average of time windows instead of single instants, for each picture.

 * Contact sheets: Allow explicit list of times in input (+ display as in MNE-Python with TS)

== Database ==
 * Save iHeadModel somewhere in the datbase structure
 *
 Generalize the use of the units (field .DisplayUnits): Save in source files
-Line 56:
+Line 192:
- * Thresholding the connectivity matrices
 * t-tests on connectivity measures
 * Graph view:
  * Fixed scales for intensity sliders
  * Text bigger
  * Too much data in appdata
  * Re-write using pure Matlab code and smoothed graphics
  * Fixed scales for intensity sliders
  * Add "=" shortcut for having graphs with similar configurations
  * Disable zoom in one region (serious bugs)
 * Coherence:
  * Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
 * Granger:
  * Crashes sometimes: improve stability
  * Re-write and optimize code
  * Add progress bar
 * PLV:
  * Add p-values
  * Remove evoked
  * Optimize code
  * Add time integration
  * Unconstrained sources
 * PAC:
  * 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
 * Other metrics:
  * Coherence by bands: bst_coherence_band_welch.m
  * Granger by bands: bst_granger_band.m
  * Inter-trial coherence
 * Multi-tapers?
 * Tutorial coherence [1xN] : Reproduce FieldTrip results?
+ * Thresholding and stat tests for connectivity matrices:
  * Panel Display: Show only the top N% measures
  *
  Misic: https://www.nature.com/articles/s41583-022-00601-9

  *
  {{attachment:connect_toolboxes.jpg}}


 * Connect NxN display:
  * Graph on sensors: does not place the sensors correctly in space
  * Display as image: Add legend of the elements along X and Y axis
  * Display as time series: Display warning before trying to open too many signals
  * Optimize display: use surface() instead of line() for links? (as in figure_3d/PlotFibers)

 * Time-resolved correlation/coherence: Display as time bands
-Line 92:
+Line 210:
- * ICA:
  * Exploration: Add window with spectral decomposition (useful for muscle artifacts)
  * Comparison JADE/Infomax: <<BR>> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135
  * Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)
  * Dimension reduction with PCA adds artifacts: Not done by default in EEGLAB<<BR>>Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )<<BR>>Student Carl Leichter detailed this in his thesis
  * S Makeig: Use ICA to select the IC of interest instead of only removing artifacts
 * Distributed processing: Brainstorm that can run without Java
 * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Allow processes in Python and Java
 * Call FieldTrip functions from pipeline editor
 * Optimize opening time for the menu "Add process"
 * SSP:<<BR>>
  * Display warning if changing the ChannelFlag while there is a Projector applied
  * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
 * Bandpass:
  * Offer option: bst_bandpass_fft / bst_bandpass_filter
  * Rewrite without the forced low-pass filter at Fs/3
  * Show warning when using inappropriate high-pass filter (precision too high)
  * Use FIR filter
 * Spectral flattening (John):
  * ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis

 * PSD:
  * Rewrite to have the same input as coherence

  * Normalize with the total power (TF/sum(TF,3))
 * Remove line noise: http://www.nitrc.org/projects/cleanline
 * Interpolate the bad channels
 * Band-limited power envelope
 * Reports:
  * Save as HTML / PDF
  * Do not display the intermediate files
+ * Add MNE-Python functions:
  * scikit-learn classifiers
  * BEM single layer (John wants to test it)
  *
  ICA: https://neuroimage.usc.edu/forums/t/ica-on-very-long-eeg/23556/4

  *
  https://neuroimage.usc.edu/forums/t/best-way-to-export-to-mne-python/12704/3

  * Reproduce other tutorials / examples
  *
  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

 *
 Chronux toolbox : http://chronux.org/

 *
 Add FieldTrip functions:

  * ft_sourceanalysis:
   * Check noise covariance
   * Check all the options of all the methods
   * Single trial reconstructions + noise covariance?
   *
   Filters?? http://www.fieldtriptoolbox.org/example/common_filters_in_beamforming

   *
   Beamformers: Save ftSource.avg.mom <<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:
  *
  Test speed for writing files: <<BR>>https://undocumentedmatlab.com/articles/improving-fwrite-performance

  * Use CUDA for speeding up some operations (filtering, wavelets, etc)
  * Use Matlab Coder to optimize: Wavelets, bandpass filter, sinusoid removal
-Line 125:
+Line 268:
+  * Bug: After "convert to continuous", the time of the following processes should change
-Line 126:
+Line 270:
+  * 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

 *
 Remove line noise: http://www.nitrc.org/projects/cleanline
-Line 127:
+Line 279:
-  * Standardize using: diff before calculation + cumsum (checkbox "flatten data")
  * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  * Display logs as negative
  * 2D Layout in spectrum
  * Make much faster and more memory efficient (C functions coded by Matti ?)
  * TF scouts: should display average of TF maps
 * Artifact detection:
  * Detection of bad segments in the RAW files (Beth)
  * Artifact rejection like SPM: if bad in 20%, bad everywhere
  * Test difference between adjacent samples
  * Allow the detection on differences of signals (bipolar montages)
 * Average:
  * Remember how many trials were used per channel
  * Save standard deviation
  * Display standard deviation as a halo around the time series
 * Co-registration of MEG runs:
  * SSP: Group projectors coming from different files
  * Finish validation of the method
  * Apply to continuous recordings for correcting head movements
 * Resample continuous files
 * Current Source Density (CSD) => Ghislaine<<BR>>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html
 * Other processes:<<BR>>
  * 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)

== Database ==
 * Optimize startup speed
 * Start Brainstorm without Java (-nodesktop)
 * Sort files by comment
 * MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
 * Group matrix files => allow to process matrix files by trial types

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

 * Screen captures: save straight to the database

 * Rename multiple files

 * Allow matrix files to be attached to other files

== 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/
+  * Optimization: bst_timefreq (around l.136),  remove evoked in source space: Average should be computed in sensor  space instead of source space (requested by Dimitrios)
  *
  Short-time Fourier transform: http://www.mikexcohen.com/lectures.html

  * Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead.
  * When normalizing with baseline: Propagate with the edge effects marked in TFmask
  * Allow running TF on montages
  * Review continuous files in time-frequency space (for epilepsy)
  * Bug when computing TF on constrained and unconstrained scouts at the same time (in mixed head models for instance): uses only the constrained information and doesn't sum the 3 orientations for the unconstrained regions.


== Anatomy ==
 *
 Import SimNIBS4: Use final_tissues_LUT.txt instead of fixed list of tissues: https://neuroimage.usc.edu/forums/t/removing-a-lesioned-area/38414/20

 *
 Simple-brain-plot: https://github.com/dutchconnectomelab/Simple-Brain-Plot


 * MNI normalization: More options:
  * DARTEL / SHOOT
  *
  BrainSuite (wait for Anand)

  * Import from SimNIBS (Conform2MNI_nonl.nii.gz, MNI2Conform_nonl.nii.gz)


 * MRI Viewer:
  *
  Adjust CT contrast better: https://neuroimage.usc.edu/forums/t/automatic-localization-of-seeg-electrodes/36302/10

  * 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


 * Defacing:
  *
  https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html

  * Removing MNI face mask using MNI coordinates

 * Atlas switch in 3D MRI figures
 *
 Bug import anatomy: Requested nVert > high-resolution cortex surface: Creates an empty cortex_0V

 *
 BrainSuite:

  * Use same colors for left and right for anatomical atlases
  * Use for volume coregistration (rigid / non-rigid)
  * USCBrain: Add default electrodes positions
  *
  Remove BrainSuite1 when not needed anymore


 * Brain2mesh: Add import of 10-10 positions
 * Templates for different ages:
  *
  MNI: https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1

  *
  Pediatric head atlases: https://www.pedeheadmod.net/pediatric-head-atlases-v1-2/


  *
  https://iopscience.iop.org/article/10.1088/2057-1976/ab4c76

  *
  https://www.biorxiv.org/content/biorxiv/early/2020/02/09/2020.02.07.939447.full.pdf

  *
  John Richards: https://www.nitrc.org/frs/?group_id=1361

  *
  Neurodev database: https://jerlab.sc.edu/projects/neurodevelopmental-mri-database/

  *
  https://openneuro.org/datasets/ds000256/versions/00002

  *
  https://osf.io/axz5r/



 * Scouts:
  * Display edges in the middle of the faces instead of the vertices

 * Parcellating volume grids: scikit-learn.cluster.Ward
 *
 Geodesic distance calculations:<<BR>>https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching

 * Improving the registration between EEG and anatomy templates:
  * Warping: Improve the basic alignment of the digitized electrodes on the templat, possibly with Cz and other anatomical landmarks
  * EEG template positions: rework using a standardized Cz position (+ other landmarks)


== Forward modeling ==
 * DUNEuro/FEM:
  *
  Add lesion mask to SimNIBS: https://simnibs.github.io/simnibs/build/html/documentation/command_line/add_tissues_to_upsampled.html#add-tissues-to-upsampled-doc

  *
  GeomtryAdapted: Buggy?

  *
  Display differences between leadfields: amplitude of difference (right-click > Compare)

  * Display sensitivity on FEM surface

 * OpenMEEG: Detect bad results + exclude from leadfield
 * BEM single sphere: Get implementation from MNE
 * Add eyes models to attract eye activity
-Line 185:
+Line 400:
+ *
 Reproduce results in "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x

 * eLORETA instead of sLORETA?
  *
  https://neuroimage.usc.edu/forums/t/compute-eeg-sources-with-sloreta/13425/6

  *
  https://neuroimage.usc.edu/forums/t/loreta-and-source-localization/30525

  *
  "eLORETA  algorithm  is  available  in  the  MEG/EEG Toolbox of Hamburg (METH)": https://www.biorxiv.org/content/biorxiv/early/2019/10/17/809285.full.pdf

  *
  https://github.com/brainstorm-tools/brainstorm3/issues/114


 * 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 186:
+Line 426:
-  * Finish dipole scanning (allow the tab to control multiple figures separately)
  * Dipole fitting: We will not implement non-linear fits, recommended use of dense volume grids
+  * Display dipoles in MRI viewer
-Line 189:
+Line 428:
-  * Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates
 * Panel Get coordinates: Add button "find maximum"
 * Create scout form maximum: Not available yet for mixed/volume head model.
 * Stenroos 2014 paper: Include the following methods
  * Inner and outer skull surfaces generator from FieldTrip (needs SPM, probably not so different from BST)
  * 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:
  * Compute unconstrained and then project on the normal ?
  * Difference and stat should be: norm(A) - norm(B)
  * Stat and connectivity: what to do? (re-send email John+Sylvain)
 * Overlapping spheres: improve the estimation of the spheres for the frontal lobes
+ * Project sources: Very poor algorithm to project sub-cortical regions and cerebellum
 * Maximum:
  *
  Menu Sources > Maximum value: Doesn't work with volume or mixed head models

  * Panel Get coordinates: Add button "find maximum"
  *
  Sources on surface: Display peak regions over time (time = color) => A.Gramfort
-Line 205:
+Line 440:
-  * Test volume sources with all the subsequent processes (timefreq, stat...)
-Line 208:
+Line 442:
- * 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
 * 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
 * Display volume scouts and surface scouts at the same time
 * Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
 * BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
 * Hui-Ling beamformers:
  * More explanations about what is in NAI and Spatial filters
  * Explain that is this is better to study effects extended in time (Ntime > Nsensors)
  * Group LCMV+MCB
  * Condition LEFT median nerve: very bad results
 * Menu Sources > Simulate recordings:
  * Do not close the 3D figures after generating a new file
  * Add a process equivalent to this menu

== Anatomy ==
 * Project all sub-cortical structures to default anatomy
 * Warping: Scale option has to be fixed, it is currently very unstable
 * Scouts:
  * Display edges in the middle of the faces instead of the vertices
  * Project scouts betweens subjects and between hemispheres
  * Display scouts in a tree: hemisphere, region, subregion
  * Downsample to atlas: allow on timefreq/connect files
  * Sort scouts by region in process options
 * Co-register MRI and CT for electrodes marking in the MRI Viewer
 * Generate mixed density surfaces
 * Import / registration:
  * Major bug when importing surfaces for an MRI that was re-oriented manually
 * Use mid-gray instead of pial surface?
 * Smooth surface: Fix little spikes to irregularities in the mesh
 * Menu head model > Copy to other conditions/subjects (check if applicable first)
 * Add cerebellum to default model generated with "Import FS anatomy"
 * Add eyes models to attract eye activity
-Line 257:
+Line 445:
- * ANOVA: Use LENA functions
+ * Stat on unconstrained sources?
 *
 Stat/time series: Hide lines going down to zero (Dimitrios: https://neuroimage.usc.edu/forums/t/common-source-activation-across-subjects-and-conditions/1152/21)

 * Cluster stat: Add frequency selection option
 * ANOVA:
  * Write panel similar to Process1 and Process2
-Line 260:
+Line 454:
- * Permutation tests:
  * t-test only (wilcoxon? sign-test?): paired, equal var, unequal var
   * http://www.adscience.fr/uploads/ckfiles/files/html_files/StatEL/statel_wilcoxon.htm
   * http://www.mathworks.fr/fr/help/stats/signrank.html
   * Less powerful than t-tests
  * nb permutations ~ 1000
  * maximum statistic over "time" or "time and space"
 * Permutations / clustering: cf fieldtrip
  * http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock
  * http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq
  * Maris, Eric & Oostenveld, Robert. "Nonparametric statistical testing of EEG-and MEG-data."
 * Threshold  in time: keep only the regions that are significative for contiguous  blocks of time, or over a certain number of time points<<BR>> => Process that creates a static representation of a temporal window
 * t-test on volume sources
 * Paired t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo
  * 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
 * Create icons for Stat/PAC, Stat/Sprectrum, etc.
 * One sample t-test across subjects
+ *
 Multivariate stim-response analysis: https://github.com/mickcrosse/mTRF-Toolbox
-Line 284:
+Line 460:
- * Finish MINC/CIVET integration (finir lecture MINC2: P Bellec)
  * Send email to CIVET mailing list when done
 * FieldTrip structures: In / Out (see fieldtrip/utilities/ft_datatype_*)
 * EEG File formats:
  * EEG CeeGraph
  * EGI: Finish support for epoched files (formats 3,5,7)
 * BCI2000 Input (via EEGLAB plugin)
 * EEGLAB import:
  * Selection of conditions in script mode
  * Support for binary AND epoched files (now it's one or the other)
  * Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
 * BST-BIN: Add compression
 * Review raw on all the file formats (ASCII EEG and Cartool missing)

== Distribution & documentation ==
 * Document iEEG in "What's new"
 * Rewrite basic 12+3 tutorials: group in one series
  * Illustrate 2D Layout
  * Illustrate unconstrained sources
 * Cleaning threads on the forum
 * Add Help buttons and menus (in popups, dialog windows...) => Links to the website.

 * Publication list: Fold by years
 * Finish existing tutorials:
  * Dipoles
  * Auditory: Extend to MNE/EEGLAB/SPM
  * Auditory: Finish scripts
  * Group MEM/Epilepsy + Epilepsy tutorials
 * New tutorials:
  * MEG connectome
  * Scrambled faces (SPM/MNE-Python)
  * Describe all the processes
  * Statistics
  * Coherence (cortico-muscular ?)
  * Intra-cranial recordings (Average ref by groups using Comment field)
  * Co-register MEG runs (Beth)
 * Missing in the introduction tutorials:
  * Volume scouts
  * First steps: Brainstorm preferences
  * First steps: Temporary folder
  * Exploration: Clusters
  * Headmodel: explain the fields + how to get the constrained leadfield
  * Sources: Model evaluation (by simulating recordings)
  * Sources: Theshold min. size (not documented yet)
  * Time-frequency: Description of "log freq scale" option
  * Modify a structure manually: Export to Matlab/Import from Matlab
 * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
 * Missing in page "Cite Brainstorm": Add all the methods used in the software
 * Reference tutorials on Google scholar
+ * BIDS import:
  * Add option to process to specify the protocol name
  * Full support for iEEG and EEG
  * Disable logging of sub-processes (reloading the previous report should only show process_import_bids)
  * Read real fiducials (OMEGA) / transformation matrices:
   *
   https://groups.google.com/g/bids-discussion/c/BeyUeuNGl7I

   *
   https://github.com/bids-standard/bids-specification/issues/752#issuecomment-795880992

   *
   https://github.com/brainstorm-tools/brainstorm3/issues/139


  * Use BIDS-Matlab?

 * Test datasets:
  * See list of test datasets in process_import_bids.m
  * ds004085 / ds004473: Check response epoch + BUG with coordinate interpretation

 * BIDS export:
  * EEG, iEEG: Add events.tsv, channel.tsv, electrodes.tsv
  * Anatomy: Add t1w.json (including fiducials)
  * Use BIDS-Matlab?

 * EDF+ reader: Add resampling of channels with different sampling rates
 *
 Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284

 * DICOM converter:
  * Add dcm2nii (MRICron)
  * Add MRIConvert

 * SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
 *
 EEG File formats:<<BR>>

  *
  XLTEK: https://github.com/danielmhanover/OpenXLT

  *
  Persyst .lay: https://github.com/ieeg-portal/Persyst-Reader

  *
  Nervus .eeg: https://github.com/ieeg-portal/Nervus-Reader

  *
  Biopac .acq: https://github.com/ieeg-portal/Biopac-Reader

  * BCI2000 Input (via EEGLAB plugin)

 * 4D file format:
  * Use reader from MNE-Python: mne.io.read_raw_kit  (skip Yokogawa slow library)
  * Reference gradiometers: Keep the orientation of the first or second coil?
  * Reference gradiometers: Add the sensor definition from coil_def.dat
  * Validate with phantom recordings that noise compensation is properly taken into account
  * The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
  * 4D phantom tutorial (JM Badier?)

 * BST-BIN: Add compression to .bst
 * MINC MRI: Add support for "voxel to world" transformation (vox2ras) similarly to .nii

== Distribution ==
 * Java-free Matlab: All references of functions below must be removed
  *
  '''JavaFrame''': screencapture.m (used for screen captures of videos)

  *
  '''Actxcontrol''': Used for video-EEG

   *
   uihtml + JavaScript callbacks?

   * ActiveX in .NET app?
   * Pure Java framce + VLC java plugin?
   * Other video player?

  *
  '''Javacomponent''':

   * mri_editMask
   * figure_mri
   * process_bandpass

  *
  List .jar files used from Matlab distribution (e.g. dom) => Check all the import calls


 *
 Cleanup GitHub repository:

  *
  https://github.com/brainstorm-tools/brainstorm3/issues/473

  * Remove ICBM152 default anatomy from repo
  * Move external I/O libraries as plugins:
   * mne-matlab
   * CEDS64ML
   * edfimport
   * eeprobe
   * son
   * ricoh
   * yokogawa
   * easyh5



== Documentation ==
 * All tutorial datasets in BIDS (including introduction tutorials)
 * Deface the MRIs of all the tutorials
 *
 Count GitHub clones in the the download stats

 * MNE-Python 1.0: Test and update install documentation
 * Tutorial OMEGA/BIDS:
  * Update the organization of derivatives folder (full FS folders)
  * 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

  *
  Reproduce tutorials from MNE-Python: https://martinos.org/mne/stable/tutorials.html

  *
  Cam-CAN database: https://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/<<BR>>(download new datasets, including maxfiltered files and manual fiducial placements)

  * MEG steady-state / high-gamma visual / frequency tagging
  *
  Reproduce results from "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x

  * Stand-alone ICA tutorial
-Line 335:
+Line 603:
- * Workshops:
  * Create scouts doesn't work: scout created on the other side of the brain
  * Import anatomy folder: Out of memory on Win 32bits (restart Matlab)
  * Compute head model: Out of memory on Win 32bits
  * Bandpass filter: Out of memory (Auditory workshop)
 * Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz)
  * Cannot import two .ds folders at once
  * Colors inverted in the PSD/TF plots (power vs. log)
  * Cannot type the name of a channel in "Detect ECG"
 * Image viewer: Difficult to get to 100%
 * Canolty maps computation: Fix progress bar
 * Smooth TF windows that contain multiple plots
 * Record tab: Text of epoch number is too big on MacOS
 * in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
 * tree_dependencies: sources files, reprojected on default anatomy; If  based on data files that are bad trials, they should be ignored by  tree_dependencies, and they are not
 * Image viewer has some bugs on some systems
 * Screen capture when there is a fading effect in the window manager: captures the window
 * Close figure with coherence results should hide the "frequency" slider
 * Edit scout in MRI: small modifications cause huge increase of the scout size
 * Reports: Text size is too small with Java 1.5 (2006b-2007a)
 * Optimize MRI viewer with patch() instead of image()
 * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
 * 2DLayout (time series):
  * Sometimes the lines are not visible
  * Does not work when DC offset is not removed
 * 2DLayout (TF): Images are too far apart with EEG 20 channels
 * Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
 * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG.
+ * Image viewer:
  * Difficult to get to 100%
  * Buggy on some systems

 * 2DLayout:
  * (TF) Units are weird with % values
  * (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling

 * Progress bar:
  * Doesn't close properly on some Linux systems
  * Focus requests change workspace when processing constantly (Linux systems)


== Distributed computing ==
 *
 Options from FieldTrip:

  *
  Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer

  *
  Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine

  *
  Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub

  *
  Documentation: https://www.fieldtriptoolbox.org/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/


 *
 PSOM: http://psom.simexp-lab.org/

 *
 Google: https://www.youtube.com/watch?v=LLMXV3o2FT0

  *
  https://edu.google.com/why-google/case-studies/unc-chapel-hill-gcp/
-Line 365:
+Line 645:
- * Hide Java panels instead of deleting them
 * mri2scs: convert arguments to meters
 * Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (Matlab 2014b)
 * bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
 * Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow)
 * Optimize bst_get:
  * Now study and subject have necessarily the same folder name
  * Replace big switch with separate functions
 * Progress bar:
  * Add different levels (to handle sub-processes)
  * Make work correctly with RAW on resting tutorial
  * Uniformize calls in bst_process/Run
  * Add a "Cancel" button
 * 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
 * in_bst_results (isFull=1): DataFile should be relative
+ * Replace all calls to inpolyhd.m with inpolyhedron.m (10x faster)
 *
 Interface scaling: Rewrite class IconLoader to scale only once the icons at startup instead of at each request of an icon (might improve the speed of the rendering of the tree)

 * Processes with "radio" and "radio_line" options: Replace with "radio_label" and "radio_linelabel"
 * Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)

Software

Users

Development

What's next

Recordings

ECOG/SEEG

Pre-processing

Reproducibility toolbox

Interface

Database

Connectivity

Processes

Anatomy

Forward modeling

Source modeling

Statistics

Input / output

Distribution

Documentation

Current bugs

Distributed computing

Geeky programming details