NeuroAnalyzer roadmap

High priority entries are marked with of !!. Items that are still considered are marked with ?.

General

• !! what will happen if exclude_bads is true and all ch is in bads
• ? replace Gtk.jl with Gtk4.jl
• ? replace Plots.jl with GLMakie.jl
• ? separate plot_*() into plot_*_cont() and plot_epoch_*()
• ! better documentation
• !! better code comments
• ! more performance optimizations
• ! distributed computing for pipelines
• !! improve support for MEG data
• ! improve support for ECoG data
• ! improve support for NIRS data
• ! support for IEEG data
• ! support for SEEG data
• ! use eyetracker to detect eye movement and blink artifacts
• ? use 3D scanner for head mesh, e.g. Polhemus
• ? use 3D tracker for electrode locations, e.g. Polhemus
• ? organize data using BIDS standard – should this be internal or external?
• ! NeuroStim: TES modeling
• ! NeuroStim: removal of TES artifacts from EEG
• ? NeuroStim: transcranial focused ultrasound (tFUS)
• ? NeuroStim: transcranial infrared laser stimulation (TILS)
• ! NeuroTester: visual / auditory stimuli presentation module
• ! NIRS: add channels locations in the middle of optodes
• ! NIRS: head plot in topoplot
• ! more interpolation methods

IO

• ! better auto-detection of file format
• ! more import formats
• ! NWB:
  • check .TSV naming scheme
  • check .JSON naming scheme
  • check how mixed (EEG/IEEG/SEEG) recording is handled
  • check STIMULI vs EVENTS

Edit

• ! automated channel rejection
• ! automated epoch rejection
• ! insert channel

Process

• !! reference_custom() should calculate position of channels and add them to locs
• ! automated cleaning of artifacts
• ! REST referencing
• ! multitaper: generate frequency-band-selective tapers to increase sensitivity, varying the length of time segments, varying the number of tapers and central frequency of the spectral representation of the tapers

Analysis

• !! add more estimators to entropy() and mutual_information() (see https://github.com/Tchanders/InformationMeasures.jl)
• ! ierp() – based on ERPLAB
• ! wavelet-based coherence
• ? reports in .md format (use Pandoc to convert to HTML/ODT/DOCX/PDF)
• ? ANOVA test for segments
• ! CDR: current density reconstruction (GCDR, CDR spectrum), activity within specified band
• ! frequency bands: medial vs left vs right channels within each band
• ! source localization
  • dipoles
  • beamforming, leakage correction
• ! FOOOF
• ! import and process MRI data for EEG source localization
• !! connectivity:
  • neural Granger causality (NGC)
  • phase synchronization measurements: phase coherence (PC)
  • cross-frequency phase-amplitude coupling
  • phase-amplitude cross-frequency coupling (PAC)
  • power envelope connectivity
• ! probability maps: the local likelihood of belonging to a given population
• ! signals/PSD comparison
• ! tensor and other statistical maps (magnitude and direction, probabilistic regions, regions of high vs low variability)
• ! support for clusterDepth.jl
• ! support for Unfold.jl/UnfoldMakie.jl

Plots

• !! plot TES/TMS protocols
• !! fix: do not plot deleted NIRS channels
• ! click on the component to select it in iplot_icatopo()
• ! click on the PSD to enlarge it in plot_psd(type=:topo)
• !! improve plot_locs() for NIRS
• ! brain topography
• ! connectome graph
• ! 3d head/brain surface plots
• ! coherence spectrum (y: relative amplitude, x: frequencies)
• ! ITPC topoplot
• ! plot OBJ + component