NEWS

ieegio 0.1.0 (2026-05-31)

Added burn_curve to burn electrode trajectories (e.g. depth/sEEG leads or DBS shafts) into a volume given start and end positions in image native RAS coordinates, with configurable radius and per-segment colors
Added a merge mode to burn_curve so newly burned trajectories can be composted onto an existing volume instead of overwriting it
Added a base R graphics plot method for ieegio_surface objects as an alternative to the default r3js rendering, useful for static figures and environments without WebGL
Fixed get_channel so channels can be looked up by label (in addition to index) for BCI2000 and BrainVision formats
Fixed mat_to_quaternion to correctly handle handedness changes, aligning the quaternion sign convention with FreeSurfer
Code style and lint cleanup across the package; rebuilt documentation

Fixed CRAN check issues
Added volume and surface related functions as MCP tools (can be loaded via package ravepipeline and ellmer)

Added new_space and as_ieegio_transform to define coordinate spaces and chain transforms
Added io_read_ants_transform to read ANTs affine and displacement field transforms
Added io_read_flirt_transform to read FSL FLIRT affine transforms
Added volume_to_surface and surface_to_surface for mapping data between volumes and surfaces
Fixed point transform ambiguity when chaining transforms with different interpretations
Improved plot.ieegio_volume intensity windowing using percentile-based display range (2-98 percentiles), following conventions from FSLeyes, AFNI, MRIcroGL, and SPM
Auto-detection for CT vs MRI data: excludes zeros by default but includes them when lower percentile is below -500 (indicating CT with -1024 background)
Statistical overlay detection: applies symmetric range for z-score-like data
Values outside display range are now clamped to boundary colors instead of rendering as transparent

Added as_nifti_header as a workaround when RNifti is missing (not installed or running in WebAssembly)
Added automatic checks when pushing commits the repository to Github

Added LazyFST class
Fixed a bug where gzipped is ignored in io_write_nii.array
LazyH5 fall back to alternatives when HDF5 is not supported in wasm
Plotting surfaces use r3js by default
Fixed BrainVision annotation bugs
Supported writing to STL format (to support importing to BrainLab)
Added supports to read streamlines data (trk, tck, tt, vtk)
Writing to freesurfer surfaces also appends orientation information at the end.

Added merge support for both volume and surface objects; for surface objects, users can choose whether to merge the objects in model or world space
Added dependency ravetools to help speed up sample volumes using C++
Fixed missing transform issue in writing to GIfTI format
Fixed write_surface not working when writing to FreeSurfer measurement (curvature) format
Fixed a typo that caused setting volume data resulting in errors
as_ieegio_surface does not require vertices

Cleaned h5py loader
mat_to_quaternion always returns non-negative w now
Added generics dim and length to volume object
Fixed annotation issues in EDF format
Time selection is double-sided using greater equal and less equal signs
Added more sample data
Supports colored (RGB[A]) formats
Fixed color intensity when cal_min and cal_max is set
Using r3js for visualizing surfaces
Added resample_volume to sample images (currently only nearest neighbor)
Added burn_volume to burn contacts (positions given in the image native RAS coordinate) with any given colors
Fixed io_h5_names returning wrong names when using with h5py
Exported internal class LazyH5 for down-stream packages
Added as_ieegio_volume and as_ieegio_surface to enclose volume or surface data
Added a flag to disable using Python

Added h5py as an alternative back-end support
Fixed a bug where images are not loaded correctly due to image format being ignored
Fixed Torig (index to tkr coordinate transform) issue
Fixed a global variable issue
Fixed a bug where file name is not respected