MNE-CPP v2.2.1

Full Changelog: v2.2.0...v2.2.1

MNE-CPP v2.2.0

What's Changed

Highlights

• MNX as MNE Scan project storage — Pipeline configurations now load and save as .mna (JSON) or .mnx (CBOR) files via MnaIO; legacy XML pipeline format removed. Default auto-save path is default.mna.
• Unified File-menu naming across applications — mne_scan, mne_inspect, and mne_browse now use the same "Open Project… / Save Project… / Export Project as MNX…" pattern.
• MNE-C CLI parity (82 tools) — every command-line tool from MNE-C has a mne-cpp counterpart; final 4 ports landed in this release (mne_make_movie, mne_convert_lspcov, mne_convert_ncov, mne_dacq_annotator).
• Lossless MNA / MNX round-trip — every MNA struct preserves unknown JSON/CBOR keys via an extras field, so newer schema fields survive a round-trip through older software.
• Performance as a co-equal optimization goal — periodic code-optimization prompt and matching optimization-requirements.md doc cover both idiomatic-code refactors and quantitative perf wins (≥ 5 % wall-clock).

New Features

• MNA graph-execution library (mne_mna): New library for the .mna analysis node-graph format with YAML-based operator definitions, topological execution, and MnaOpRegistry for built-in and user-registered operators
• MNX binary container — CBOR-based binary equivalent of .mna (MNX1 magic header), with embedded-data support and identical key structure for lossless format conversion
• MNA Scan integration — MnaGraph m_pPipelineGraph mirrors the live plugin scene in PluginSceneManager; MnaDataKind ↔ ConnectorDataType mapping shipped in mna_scan_types; PluginGui::loadConfig/saveConfig route through MnaIO::read/MnaIO::write
• Stream-mode MnaGraphExecutor — MnaGraphExecutor::startStream() / stopStream() with StreamContext for real-time acquisition pipelines
• Machine-learning library (mne_ml): New library with MlTrainer for sklearn-compatible model training via embedded Python, supporting SVM, Random Forest, Logistic Regression, and custom estimators
• STS covariance estimators: Added Ledoit-Wolf and Oracle Approximating Shrinkage (OAS) estimators to the sts library with cross-validation support against scikit-learn
• Source-space cluster permutation tests — StatsCluster::oneSamplePermutationTest(), fTestPermutationTest(), tfce() (threshold-free cluster enhancement); StatsAdjacency::fromSourceSpaceTemporal() for spatio-temporal adjacency
• Spectral connectivity expansion — GrangerCausality ("GC"), DirectedTransferFunction ("DTF"), PartialDirectedCoherence ("PDC"); shared MVAR fitting via MvarModel
• CMNE sparse inverse: Added Cascaded MNE (InvCMNE) solver to the inverse library for spatially sparse source estimation
• DSP Infomax ICA: Extended the dsp library with an Infomax-based ICA decomposition algorithm
• BIDS coordinate system: Added BidsCoordinateSystem class for round-trip parsing and writing of coordinatesystem.json, and BidsElectrode::toFiffDigPoints() for converting BIDS electrodes to FIFF digitizer point sets
• FreeSurfer atlas lookup: Added FsAtlasLookup for Desikan-Killiany / Destrieux atlas region querying
• MRI slicer: Added MriSlicer class for extracting orthogonal slices (Axial/Sagittal/Coronal) from NIfTI volumes
• 3D electrode visualization: ElectrodeObject now includes QRhi GPU buffer management (updateBuffers, vertexBuffer, indexBuffer, instanceBuffer) following the BrainSurface pattern; new electrode.vert / electrode.frag shaders with instanced contact spheres and Blinn-Phong lighting
• 3D MRI slice visualization: New SliceObject renderable for textured MRI volume slices with voxel-to-world transforms and intensity windowing; new slice.vert / slice.frag shaders
• FiffAnnotations integration: AnnotationModel refactored to use FiffAnnotations as backing store instead of internal QVector<AnnotationEntry>, with fiffAnnotations() / setFiffAnnotations() public accessors
• Python cross-validation tests: Added GUARD_PYTHON / GUARD_PYTHON_PACKAGE macros ensuring Python-dependent tests fail in CI (MNE_REQUIRE_PYTHON=true) instead of silently skipping
• PythonTestHelper extensions: Added writeMatrix(), readMatrix(), and evalMatrixViaFile() convenience methods for Eigen↔NumPy round-trip validation
• MNA Scan plugin registry: Added scan-plugins.json schema and MnaScanTypes class for declaring MNE Scan plugins as MNA operator schemas
• W-file I/O: Added read_w and write_w methods to FiffStream for FreeSurfer .w format surface data
• Cortical surface mapping: New MNECorticalMap class with icoDownsample() for icosahedral downsampling, smoothOperator() for nearest-neighbor surface smoothing, and computeMorphMaps() for cross-subject cortical morphing
• Scalp surface generation: Added makeScalpSurfaces() to MNEBemSurface for creating decimated scalp meshes at multiple resolutions
• Processing history: Added copyProcessingHistory() to FiffStream for transferring processing provenance between FIFF files

MNE Inspect

• UI overhaul — Native QMenuBar (File / View / Tools / Help) with macOS system-menu integration, Recent Projects submenu (max 10), Ctrl+O / Ctrl+Q / Space shortcuts; closable + movable Controls and Loaded Files dock widgets with custom flat title bars; status bar with progress; saveState() / restoreState() persistence
• Loaded Files panel — live QTreeWidget with Name / Type / Path columns and context menu (Remove, Copy Path, Show in Finder); double-click STC entry activates it in the source-estimate combo
• Progressive-disclosure controls — load buttons removed from sidebar; menu actions are the single entry point; control groups disabled until matching data loads; data unload via Loaded Files context menu
• WASM compatibility — menu bar renders inline; QFileDialog guarded for WASM; recent-files menu disabled on WASM

MNE Scan

• File menu uses Project terminology — &New Project (Ctrl+N), &Open Project… (Ctrl+O, accepts *.mna *.mnx), &Save Project… (Ctrl+S, defaults .mna), &Export Project as MNX… (Ctrl+Shift+E, always binary CBOR)
• Auto-save default path — default.xml → default.mna (auto-loaded on startup if present)
• Foreign-data preservation — round-trip saves preserve unknown fields via m_loadedMnaProject
• Modernised pipeline canvas — rounded-rect nodes with gradient fills, drop shadows, type labels (SENSOR / ALGORITHM), centred name, hollow-input / filled-output ports, Bezier connections with tangent arrowheads, dot-grid background, Tailwind-inspired palette, selection glow

MNE Browse

• Project reset on standalone open — opening a raw file without a project resets m_mnxProject to prevent stale-project contamination across all 5 file-open entry points (desktop menu, WASM picker, recent files, drag-drop, CLI)

WASM Progressive Web App

• PWA manifest + service worker — scripts/wasm/manifest.json, scripts/wasm/sw.js, 192×192 / 512×512 icons; offline caching with versioned cache keys; combined COOP/COEP header injection
• No server required — deploy bundle to any static host; service worker injects required headers for SharedArrayBuffer

Command-Line Tools

• Final MNE-C CLI parity (4 new): mne_make_movie (STC frames → PNG via FsSurface orthographic projection), mne_convert_lspcov (LISP S-expression covariance → FIFF FiffCov), mne_convert_ncov (ASCII ncov → FIFF), mne_dacq_annotator (event annotation replacing legacy Motif GUI)
• Inverse tools (7 new): mne_compute_cmne, mne_inverse_pipeline, mne_label_ssp, mne_average_estimates, mne_process_stc, mne_make_uniform_stc, mne_map_data
• Preprocessing tools (7 new): mne_add_triggers, mne_change_baselines, mne_change_nave, mne_copy_processing_history, mne_fix_stim14, mne_make_derivations, mne_toggle_skips
• Info tools (6 new): mne_check_eeg_locations, mne_evoked_data_summary, mne_list_coil_def, mne_list_proj, mne_sensor_locations, mne_show_mna
• Forward tools (3 new): mne_fit_sphere_to_surf, mne_make_scalp_surfaces, mne_transform_points
• Conversion tools (3 new): mne_convert_ctf_markers, mne_epochs2mat, mne_mna_bids_converter
• Total CLI inventory: 82 tools — full MNE-C feature parity

CI/CD

• Upgraded codecov/codecov-action from v5 to v6 to resolve Node.js 20 deprecation warnings
• Added MNE_REQUIRE_PYTHON: 'true' environment variable to all platform test steps
• Added scikit-learn to Python test dependencies
• Updated lodash from 4.17.23 to 4.18.1 (Dependabot security fix)

Bug Fixes

• Fixed potential silent test skips — Python-dependent tests now respect MNE_REQUIRE_PYTHON enforcement
• Fixed deprecated qWarn calls in test_mne_source_analysis (replaced with qWarning())
• Fixed unused [[nodiscard]] return values in test_tool_inverse_computation

Documentation

• Added 26 new command-line tool documentation pages
• Comprehensive MNA / MNX format manual page (mna-format.mdx, ~692 lines) — file types, BIDS-like data hierarchy, computational graph, execution modes, parameter system, op registry, verification & provenance, MNX byte layout, schema versioning, complete annotated JSON example
• Rewrote MNA API reference page (api-mna.mdx) with full class inventory (63 → 572 lines)
• Added ML library API reference page (api-ml.mdx)
• Added Statistics library API reference page (api-sts.mdx)
• Updated tools overview with all 26 new tools and new "Inspection and Information" section
• Updated overview and API pages with Mna, Ml, Sts library entries
• Expanded glossary with 14 new terms (CMNE, DICS, LCMV, MNA, MxNE, ONNX, etc.) and 3 file format entries (.mna, `...

Development Builds

Latest development builds from the staging branch. These are pre-release builds for testing.

ONNX Runtime Artifacts

Reusable ONNX Runtime shared library packages for CI and local development.

MNE-CPP v2.1.0

What's Changed

New Features

• MNE Browse overhaul

  • QRhi-based 2D channel rendering for Metal/Vulkan/D3D12 performance
  • ICA browser with component visualization, rejection, and original-data reset
  • Epoch review workflow with evoked computation and histogram view
  • Annotation workflow with FIF interoperability and auto-merge
  • Virtual channel derivations with weighted reference workflows
  • Covariance matrix heatmap visualization and whitening controls (W key)
  • Projector dialog (J/Shift+J) and SSP toggle
  • 2D layout view with mouse-wheel zoom, auto-scale, and channel scaling spinboxes
  • Dark mode, drag-and-drop file open, recent files list
  • GPU clipping/z-score shaders, fullscreen (F11), zen mode (F)
  • Linear detrending (D key cycles None/DC/Linear)
  • GFP overlay on butterfly view
  • Interactive ruler tool with amplitude snap and semi-transparent overlay
  • Double-click bad-channel marking, click-to-toggle bad channels
  • Stimulus lane above time ruler with event markers
  • Per-description event/annotation filtering and visibility toggles
  • Channel sort by type, epoch grid lines (G), overview bar toggle (O), scroll speed control
  • Source-estimate export workflow
  • Session filtering workflow
  • Settings persistence across sessions via QSettings
  • Event file saving to FIF and ASCII formats
  • WASM loading screen and optimized WebAssembly build

• MNE Analyze Studio

  • Agent-based workflow engine with grounded LLM safety
  • Multi-provider planner profiles (OpenAI Responses API)
  • Reusable inspect 3D surface views
  • Extension-based view architecture with hosted view tooling
  • VS Code chat UX integration and .mna project format

• BIDS library (mne_bids): New library for reading and writing BIDS-formatted datasets with testframe

• Beamformers: Added beamformer classes to the inv library with testframes

• DSP library enhancements

  • WelchPsd: Welch power spectral density estimation
  • MorletTfr: Morlet wavelet time-frequency representation
  • xDAWN: xDAWN spatial filtering for ERP denoising
  • KMeans: Cosine and correlation distance normalization implemented
  • Real-time covariance: Channel picks applied (MEG/EEG only)

• Logging: Renamed ApplicationLogger to MNELogger with MNE_LOG_LEVEL and MNE_LOG_MODE environment variables

CI/CD

• Qt 6.11 support with auto-detection in init.sh
• Build Qt Installer Framework 4.11.0 toolchains from source
• Offline self-contained installers (.run, .dmg, .exe)
• Nightly WASM builds deployed alongside stable releases
• Reusable Qt toolchain assets consumed by CI workflows
• Eigen downloaded at configure time (no longer bundled)

Bug Fixes

• Fixed Metal/QRhi rendering on macOS: native window, infinite repaint loop
• Fixed butterfly whitening scale and circular channel arrangement
• Fixed 2D layout channel filtering, scale persistence, and item sizing
• Fixed crosshair repaint cascade, split MEG grad/mag scale labels
• Fixed DSP SSS and bad-channel regressions
• Fixed DSP pi constants on Windows, params defaults on Clang/GCC
• Fixed Windows linker error for nested Params struct exports
• Fixed macOS test flakiness and WASM build errors
• Fixed mne_anonymize unique_ptr usage
• Fixed ruler amplitude precision (1 → 3 decimal places)
• Fixed stim chip overlap, event line z-order, and resize resampling
• Fixed scroll pan boundary and smooth inertial scroll

Documentation

• Updated website to reflect renamed/split libraries
• Updated build guide paths (tools/ → scripts/)
• Fixed release download page for installers and WebAssembly
• Updated Zenodo DOI to 19139238

Full Changelog: v2.0.0...v2.1.0

Eigen SDK Artifacts

Reusable Eigen CMake package bundles for CI and local development.

MNE-CPP v2.0.0

Versioning

• MNE-CPP libraries: Version 2.0.0
• CLI tools (51 ported MNE-C tools, mne_dipole_fit, mne_inspect): Derive version from the MNE-CPP project version (2.0.0) via CMake compile definition
• MNE Scan: Version 1.0.0 (first stable release as a standalone application)
• MNE Analyze: Version 1.0.0 (first stable release as a standalone application)
• IConnector plugin interface: Bumped to mne_rt_server/2.0

Breaking Changes

• Library renames: connectivity → conn, communication → com, rtprocessing → dsp, inverse → inv, disp3D_rhi → disp3D
• Class renames: Inverse library classes now use Inv prefix (InvRapMusic, InvMinimumNorm, InvSourceEstimate, InvHpiFit, …)
• Moved classes: InvInverseOperator, InvMeasData, InvMeasDataSet moved from inv to mne library (as MNEInverseOperator, MNEMeasData, MNEMeasDataSet); backward-compatible forwarding headers provided
• Moved classes: FwdForwardSolution moved to MNEForwardSolution in the mne library; forwarding header in fwd/ for backward compatibility
• Removed: InvCorSourceEstimate class (superseded by unified InvSourceEstimate)
• Split: MNEMath split into Linalg and Numerics in the math library
• Moved: events library moved into mne_analyze application (no longer a standalone library)
• Qt requirement: Qt 6.10.0 minimum (Qt 5 no longer supported)
• Eigen upgrade: Eigen 5.0.1

New Features

• 51 CLI tools: Ported all MNE-C command-line tools to modern C++ with QCommandLineParser and ApplicationLogger
  • Conversion: mne_edf2fiff, mne_ctf2fiff, mne_kit2fiff, mne_brain_vision2fiff, and more
  • Forward modeling: mne_forward_solution, mne_setup_forward_model, mne_prepare_bem_model, mne_make_source_space, mne_make_sphere_bem, mne_average_forward_solutions
  • Inverse: mne_compute_raw_inverse, mne_compute_mne, mne_inverse_operator
  • Preprocessing: mne_anonymize, mne_process_raw, mne_compensate_data
  • Surface: mne_surf2bem, mne_check_surface, mne_watershed_bem, mne_flash_bem
  • Info: mne_show_fiff, mne_compare_fif_files, mne_list_source_space, mne_list_bem
  • Server: mne_rt_server
  • Simulation: mne_simulate_data
• Unified InvSourceEstimate: Single class with composition layers for grid data, focal dipoles, couplings, connectivity, positions, and metadata; includes tokenization support for streaming
• RHI-based 3D rendering: Migrated from Qt3D to QRhi pipeline with holographic rendering mode, Fresnel effects, dipole overlay, and async STC loading
• Flexible clustering: Variable cluster sizes in source space computation
• MNE Scan improvements: Plugin loading progress on splash screen, macOS app bundle icons
• LSL library modernized: Added lsl_ prefix, comprehensive tests, updated to LSL 1.17.5

Refactoring & Modernization

• Forward library (fwd): Removed ~700 lines of dead code; replaced printf → qInfo/qWarning; replaced goto → early return/lambdas; replaced C macros (ARSINH, EPS) → constexpr/inline; modernized FwdBemModel members from raw pointers to Eigen types and std::shared_ptr
• FIFF I/O consolidation: Moved duplicated FIFF reading functions to library classes (FiffStream::read_bad_channels, MNECovMatrix::read, MNERawInfo::find_meas_info)
• Thread safety: Fixed thread-unsafe static float* in MNEProjOp::project_vector using thread_local
• Network input validation: Added bounds checking in BabyMEG client byte conversion functions
• Sparse matrix crash fix: Guarded MNEHemisphere::operator== against segfault on default-constructed sparse matrices
• Copyright: Updated to 2026 across all library headers
• Qt6 serialization: Updated QDataStream version from Qt_5_1 to Qt_6_0 in rt_server
• Centralized CLI versioning: All 51 CLI tools now derive their PROGRAM_VERSION from the CMake project version (MNE_CPP_VERSION) instead of hardcoded strings
• Format specifier fix: Fixed %d → %lld for qsizetype in BabyMEG client warnings

CI/CD

• Restructured to Main-Staging-Feature branch model
• Build matrix: Ubuntu 24.04, macOS 26, Windows 2025 with Qt 6.10.0 and Qt 6.10.2
• CodeQL and Coverity static analysis (weekly)
• Code coverage tracking with 35% library threshold
• CPackIFW-based installer generation (.run, .dmg, .exe)
• WebAssembly build support

Documentation

• Docusaurus-based documentation site
• Organized CLI tools by domain category in sidebar
• Added MNE handbook reference pages (cookbook, FIFF format, sample dataset, data conversion)
• Completed Doxygen documentation for InvRapMusic, InvMinimumNorm, InvDipole

Bug Fixes

• Fixed crash in make_inverse_operator with non-surface-oriented forward solutions
• Fixed segfault in forward computation
• Fixed FIFF double I/O, make_dir EOF, write_cov packing, and source_cov kind
• Fixed MNECTFCompDataSet copy constructor member initialization
• Fixed coordinate transformation handling in 3D visualization
• Fixed inflated brain alignment and surface projection tolerances
• Fixed floating-point comparison tolerances in forward solution tests
• Fixed sphere simplex test convergence

Qt Toolchain Artifacts

Reusable Qt runtime, static, WASM and Installer Framework assets for CI.

v0.1.9

For details please see the changelog for v0.1.9.

v0.1.8

For details please see the changelog for v0.1.8.