Releases · danclab/laMEG

20 Mar 15:04

v0.1.4

91386a5

v0.1.4 Latest

Latest

laMEG v0.1.4 — 2026-03-20

This release introduces a major extension of laMEG’s inversion framework, adding sliding window EBB, an interface for EBBlayer, a new version of EBB specialized for laminar inference, and substantially improving the consistency and flexibility of the inversion API.

✨ Highlights

Time-resolved laminar inference (sliding-window EBB / EBBlayer)
This version adds full support for sliding-window inversion, enabling estimation of laminar profiles across time. This applies to both classic EBB and EBBlayer
A new tutorial demonstrates this workflow: tutorial_09_sliding_layer_ebb

🧠 Laminar modeling improvements

Explicit EBBlayer interface
This implementation exposes the full EBBlayer formulation, combining:
Independent priors (classic EBB)
Correlated sum priors (shared activity across layers)
Correlated difference priors (depth-specific contrast)
These priors are combined using ReML to adaptively explain laminar structure in the data .

⚙️ API improvements and consistency

Unified inversion interface
All inversion functions (EBB, EBBlayer, MSP, and their sliding-window variants) now share a consistent API:
n_spatial_modes supports 'auto' and 'all'
inversion_idx allows multiple inversions per dataset
Standardized handling of foi, woi, and windowing
Consistent return structure across methods
This significantly reduces friction when switching between inversion strategies.
Refactoring and modularization
Core inversion routines have been refactored into shared internal functions (e.g. _invert_ebb_base), reducing redundancy and improving maintainability.
Sliding-window and static inversions now rely on the same internal logic, ensuring consistent behavior across use cases.

🧰 Forward model flexibility
The coregister function now supports multiple forward models, including:

Single Shell (default)
Single Sphere
Local Spheres
OpenMEEG BEM
Additional surfaces (inner skull, outer skull, scalp) can also be specified explicitly, enabling more flexible head modeling pipelines .

📚 Documentation and usability

New sliding-window laminar tutorial (Tutorial 09)
Updated documentation build system (including post-install step and favicon support)
Improved doc import behavior for full module visibility during Sphinx builds

👥 Contributors
@solenegailhard — initial implementation of sliding-window inversion and tutorial

🔗 Full changelog
v0.1.3...v0.1.4

Contributors

solenegailhard

Assets 2

03 Nov 12:47

jbonaiuto

v0.1.3

ae9ae92

v0.1.3

laMEG v0.1.3 — 2025-11-03

🚀 Major New Features

Automatic scalp surface generation
convert_legacy_surfaces.py and LayerSurfaceSet now automatically generate and save scalp surfaces (outer_skin.raw.gii, outer_skin.converted.gii) using MNE’s BEM functions.
Surfaces are correctly converted to scanner RAS coordinates and stored under <SUBJECTS_DIR>/<subject>/bem/.

Improved mesh utilities

Added _fix_surface_holes() — closes small topological gaps in inflated and other surfaces using VTK’s vtkFillHolesFilter.
Added get_layer_vertices() and get_interlayer_distance() — utilities for mapping across laminar columns and computing interlayer spacing.

Head surface handling

Introduced load_head_mesh() for consistent access to scalp, inner skull, and outer skull GIFTI surfaces.
get_distance_to_scalp() and get_radiality_to_scalp() now rely on load_head_mesh().

Visualization

Added verify_coregistration() in viz.py to visualize coregistration results interactively in 3D (via k3d).

🧩 Core Improvements

coregister() now accepts custom scalp, inner-skull, and outer-skull surface filenames.
Automatically repairs holes in inflated meshes after downsampling.

Post-installation

Streamlined logging in postinstall.py (removed redundant console prints; unified logging output).

📚 Documentation Updates

Added clearer post-installation step (lameg-postinstall).

🧾 Miscellaneous

CI workflow now downloads test data from updated OSF URL (https://osf.io/hbrga/download).

Full Changelog: v0.1.2...v0.1.3

Assets 2

29 Oct 16:30

jbonaiuto

v0.1.2

75c7cdf

v0.1.2

laMEG v0.1.2 — 2025-10-29

⚙️ Installation

Moved SPM installation and k3d setup to postinstall script - lameg-postinstall.

🧰 CI

Updated GitHub Actions workflow to use new postinstall script.

Full Changelog: v0.1.1...v0.1.2

Assets 2

29 Oct 08:07

jbonaiuto

v0.1.1

f584e29

v0.1.1

laMEG v0.1.1 — 2025-10-29

🧩 Enhancements

Added new method LayerSurfaceSet.get_multilayer_vertex() for consistent vertex indexing across multilayer meshes.
Replaced VTK-based decimation with MATLAB’s reducepatch for surface downsampling.
Added a new tutorial: “Anatomical Predictors of Laminar Inference Accuracy” (tutorial_07_anatomy_inference_accuracy).

🧠 Documentation

Updated all tutorials (tutorials/tutorial_0*_*.py and notebooks) to use get_multilayer_vertex() for vertex mapping.

⚙️ Dependencies

Removed vtk dependency and added numpy-stl (v3.1.2) for STL mesh loading.
Updated numpy requirement from 1.19.5 → 1.21.6 for compatibility.

🧰 CI

Updated GitHub Actions workflow to use new test dataset.

Full Changelog: v0.1.0...v0.1.1

Assets 2

25 Oct 16:17

jbonaiuto

v0.1.0

049ab94

v0.1.0

Major Structural and Interface Update

This release introduces the LayerSurfaceSet class, a unified interface for managing, validating, and visualizing laminar surface hierarchies. All laminar surfaces are now stored under <SUBJECTS_DIR>/<subject_id>/surf/laminar, and co-registration automatically uses <SUBJECTS_DIR>/<subject_id>/mri/orig.mgz. A conversion script (convert_legacy_surfaces.py) is provided to update surfaces from earlier versions to this standardized format.

Core modules have been extensively refactored for clarity, documentation, and reliability:

surf.py: consolidated surface management and validation under LayerSurfaceSet.
simulate.py: improved documentation and argument structure for SPM-based MEG simulations.
util.py: centralizes environment and dependency checks (e.g., FreeSurfer path validation).
laminar.py and invert.py: updated to use the new surface interface.
Visualization (viz.py): new support for surface rendering via show_surface.

Documentation and tutorials have been rewritten to reflect the new data structure and API. This version marks the formal stabilization of laMEG’s laminar surface handling framework.

Full Changelog: v0.0.7...v0.1.0

Assets 2