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Changelog

All notable changes to MNE-CPP will be documented in this file.

[2.2.0] - 2026-04-25

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
  • 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
  • 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

Command-Line Tools

  • Inverse tools (7 new): mne_compute_cmne (CMNE source estimation via ONNX Runtime), mne_inverse_pipeline (MNA graph-based inverse pipeline), mne_label_ssp (SSP projectors from cortical ROIs), mne_average_estimates (weighted STC averaging), mne_process_stc (STC scale/export/copy), mne_make_uniform_stc (uniform STC for testing), mne_map_data (evoked data remapping between sensor arrays)
  • Preprocessing tools (7 new): mne_add_triggers (insert trigger events), mne_change_baselines (modify evoked baselines), mne_change_nave (modify n_ave field), mne_copy_processing_history (copy processing provenance), mne_fix_stim14 (reconstruct STI 014 from STI 001–006), mne_make_derivations (text derivation to FIFF), mne_toggle_skips (toggle raw skip tags)
  • Info tools (6 new): mne_check_eeg_locations (validate EEG positions), mne_evoked_data_summary (print evoked summaries), mne_list_coil_def (list coil definitions), mne_list_proj (list SSP projectors), mne_sensor_locations (export sensor locations to text), mne_show_mna (display MNA project contents)
  • Forward tools (3 new): mne_fit_sphere_to_surf (fit sphere to surface points), mne_make_scalp_surfaces (generate decimated scalp meshes), mne_transform_points (transform 3D points between coordinate frames)
  • Conversion tools (3 new): mne_convert_ctf_markers (CTF markers to FIFF events), mne_epochs2mat (epochs to MATLAB .mat), mne_mna_bids_converter (MNA ↔ BIDS conversion)

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
  • Rewrote MNA format manual page (mna-format.mdx) as comprehensive reference (73 → 476 lines)
  • 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, .mnx, .onnx)
  • Fixed orphaned pages (mna-format, api-mna) by adding to sidebar navigation
  • Added zero-tolerance warning policy to development conventions

[2.1.0] - 2026-04-10

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

[2.0.0] - 2026-03-20

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