Skip to contents

Changelog

Source: NEWS.md

ravecore 0.1.2

New Features

  • Added yael_macaque() and macaque support in the YAEL preprocessing pipeline (#32dcb87, #6c864e2).
  • Added generate_atlas_YBA() to morph YBA690 / YBA696 atlases from the MNI152 symmetric template to the subject, with an atlas-overlay report (#f45c574).
  • Added streamline support: rave_brain() gains a streamlines argument, and the YAEL process can generate streamlines from a template (#fbd913a, #f79c06e, #6adff48).
  • yael_preprocess() accepts additional_images so that more image modalities can be used for co-registration (#e6d97ba).
  • Added realign_trials() to realign arrays by event; event can be an event string or a column name such as "Time" or "Event_*" (#f4fc653, #db09e00).
  • Added validate_condition_groupings() to validate and clean condition-group lists; the epoch table is ordered by trial number (#923c913, #509570b).
  • Added "db_zscore" baseline method to power_baseline() (#ea95dc4).
  • Repositories gain get_electrode_coordinate() to subset the electrode table by channel numbers and types (#9c7f5df).
  • RAVEEpoch supports an ExcludedHint column and an exclude_trials() method; saving produces a trimmed _OutlierRemoved epoch (#33c828c).
  • Added reg3d_rigid() and cmd_run_reg3d_rigid() to rigidly co-register CT to MRI with the built-in ravetools::register_volume3d() (YAEL-reg3d; no external program needed), with Rigid, DenseRigid and FastRigid presets and mutual-information or cross-correlation cost; images with a side of 384 voxels or more are also saved as down-sampled copies for viewers. Requires ravetools 0.3.1 or later.
  • Added YAELProcess$write_talairach_xfm() to write ants/mri/transforms/talairach.xfm from an existing template normalization.

Bug Fixes

  • YAELProcess$construct_ants_folder_from_template() wrote ants/mri/transforms/talairach.xfm from the template-to-native ANTs affine without inverting it or converting LPS to RAS, and applied the MNI152-to-MNI305 correction to every template. For subjects without rave-imaging/fs, MNI305/MNI152 electrode coordinates derived from this file could be off by several centimeters. The transform is now inverted, converted to RAS, and corrected only for MNI152 templates; failures are logged and the stale file is removed. To repair a subject, run as_yael_process("<project>/<subject>")$write_talairach_xfm("<template>"), then re-save the electrode localization, or re-import an electrode table without the MNI305_*/MNI152_* columns (or with them set to zero); existing MNI columns are kept as they are.
  • cmd_run_dcm2niix() now remembers the imported image source under the yael_preprocess module (it used the old module ID surface_reconstruction), as a path relative to the subject’s raw folder (or BIDS raw folder), so the module loader can select it (#57c7684).
  • Subject pipeline listing is backward compatible with old pipeline paths, and listing all pipelines works again (#f428fc0, #e9ebb8e, #7922564).
  • filearray partitions are created before parallel workers start during power baseline, preventing a rare write race (#9dadfec).
  • rave_slices is no longer copied when normalization fails (#2dd9c41).
  • Fixed a read_mat2() call signature in the per-channel HDF5/MATLAB importer (#6872bfc).
  • Fixed a syntax issue in the YAEL process (#61016f5).

Other Changes

  • Added tests that check function-call signatures through asNamespace() (#633cde9).

ravecore 0.1.1

CRAN release: 2026-04-02

New Features

  • Added generate_atlases_from_template() to generate brain atlases from a template; supports exporting STL meshes in LPS coordinates (#d2b0f60, #c42dbb9).
  • Added use_antspynet option in the YAEL preprocessing pipeline (#7795023).
  • Added snapshot report for projects and subjects (#f91eb3b).
  • Added install_openneuro() helper to install OpenNeuro subjects (#1cdffc2).
  • Added quick mode for faster subject preparation (#70388b4).
  • Added spike diagnostic plots and graphic options for the spike visualizer (#b53887d, #f1cc332).
  • Added debug message output for spike sorter workflows (#fc25b2f).
  • Added utility functions for SpikeInterface integration (#71db36d).
  • Spike analyzer now uses band-passed signal for improved accuracy (#bb021d4).
  • Parallel workers are used to save spike data (#b4c1b46).
  • Python environment is auto-installed when missing (#5985f46).
  • Spike sorters are now cached to avoid redundant computation (#2068ce0).
  • Baseline firing rate computation now supports sub-1 rates (#292f2fe, #48f3760).
  • Spike histogram bins now cover the entire epoch range (#d49f9db, #a9e94ea).
  • Spike train is filtered to ensure times are within the requested bin range (#ca2c1e4).
  • Repository object format has been updated and improved (#ea2513a).

Bug Fixes

  • Fixed HDF5 links not being closed promptly, which could cause resource leaks (#a5e95fe).
  • Fixed LFP_reference serialization error and added additional validation checks (#93ad452, #f39f51a).
  • Fixed error message displayed when rpymat is not configured (#ff5a6b2).
  • Fixed ensure_py_package() to install spikeinterface via pip correctly (#1bcd358).
  • Fixed ordering issue when the electrode table is empty (#37904c3).
  • Fixed syntax errors (#fb14366).
  • Handle missing electrodes gracefully (#3f6e381).
  • threeBrain template is now ensured without throwing an error (#f91eb3b).
  • Invalid projects now display without broken links (#048c91e).
  • Spike iteration now processes per channel instead of manually computing iteration chunks (#1580465).
  • Only spike data (not raw signals) is stored during sorter runs (#2aa1cff).
  • Reference path is now correctly prioritized (#39c75bb).

Other Changes

  • Lint and code style improvements (#afae460).
  • Minor documentation fixes (#990fc40).
  • CRAN submission comment fixes (#004b775, #8804222).

ravecore 0.1.0

CRAN release: 2025-09-23

  • Initial CRAN submission.