Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of osl-ephys

osl-ephys - v2.3.1

Version fixes only

- Python
Published by matsvanes about 1 year ago

osl-ephys - v2.3.0

This release upgrades Python to 3.12 and MNE to 1.9.0

What's Changed

  • Release v2.2.0 by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/401
  • Matsvanes patch 1 by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/402
  • Update glmsensorsolution.py by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/403
  • Upgrade: Python 3.12 + MNE 1.9 by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/404

Full Changelog: https://github.com/OHBA-analysis/osl-ephys/compare/v2.2.0...v2.3.0

- Python
Published by matsvanes about 1 year ago

osl-ephys - v2.2.0

Summary of changes: * Improved FreeSurfer source recon * Improved linear inverse modelling * improved reports (incl. help) * ica_label fixes * Tutorial updates

What's Changed

  • Release 2.1.0 by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/377
  • Fixed logging by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/378
  • Volumetric MNE Source Reconstruction by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/379
  • Fixed bug in generating the source report. by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/380
  • EEG pipline with structurals by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/384
  • dask upgrade requirements by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/387
  • Fix: don't generate a source reconstruction report page for failed runs by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/391
  • Tested on Nottingham OPM data by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/392
  • Preproc tutorials, report, ica_label, source recon improvements by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/395
  • Docs improvements by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/396
  • enable reading different file types by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/398
  • fix preproc manual tutorial by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/399
  • AQ Workshop Changes by @AJQuinn in https://github.com/OHBA-analysis/osl-ephys/pull/394
  • feat: local parcel orthogonalisation by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/400

Full Changelog: https://github.com/OHBA-analysis/osl-ephys/compare/v2.1.0...v2.2.0

- Python
Published by matsvanes about 1 year ago

osl-ephys - v2.1.0

What's Changed

Summary - add source recon functionality, including FreeSurfer utils, Mimimum norm methods, etc. - add glm wrappers for the preproc config - add OPM utils, e.g., dealing with headshape points - add toolbox paper scripts to examples

Details * Release v2.0.0 by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/359 * fix osl>oslephys in docs by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/360 * Fix report/log directory path. by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/362 * add savepolhemusfif by @neurofractal in https://github.com/OHBA-analysis/osl-ephys/pull/364 * Fixes and Improvements for RHINO by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/370 * work in progress for adding freesurfer/surface/minimum norm source recon by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/368 * Update example freesurfersource_recon.py by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/371 * Add GLM wrappers to preprocessing by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/372 * Improved functions to get leadfields and LCMV weights by @cgohil8 in https://github.com/OHBA-analysis/osl-ephys/pull/374 * added toolbox paper scripts by @matsvanes in https://github.com/OHBA-analysis/osl-ephys/pull/356 * Add utils to downsample and standardise digitised headshape points by @neurofractal in https://github.com/OHBA-analysis/osl-ephys/pull/376 * change size of headshape points based on their number in coreg display by @neurofractal in https://github.com/OHBA-analysis/osl-ephys/pull/375

New Contributors

  • @neurofractal made their first contribution in https://github.com/OHBA-analysis/osl-ephys/pull/364

Full Changelog: https://github.com/OHBA-analysis/osl-ephys/compare/v2.0.0...v2.1.0

- Python
Published by matsvanes over 1 year ago

osl-ephys - v2.0.0

Renamed project: osl -> osl-ephys

- Python
Published by cgohil8 over 1 year ago

osl-ephys - v1.1.0

What's Changed

  • Change license to Apache 2.0
  • massive update of the documentation
  • improvements in glm_epochs and glm_base, particularly regarding stats and plotting
  • Ability to run group analysis in run_proc_batch
  • Automatic saving of each user defined key in dataset[key] (run_proc_chain/batch)
  • Add random seed to preprocessing and source_recon modules.
  • improve ica_label (keep ecg/eog on top) and create ica_apply
  • Improve report (formatting, navigation)
  • improve logs (added extra info, time stamps, random seed, ica label info, etc)
  • added features for epoching source reconstructed data

Full Changelog: https://github.com/OHBA-analysis/osl/compare/v0.1.0...v1.1.0

- Python
Published by matsvanes over 1 year ago

osl-ephys - v1.0.0

First release with the new directory structure, see https://github.com/OHBA-analysis/osl/pull/320.

- Python
Published by cgohil8 almost 2 years ago

osl-ephys - v0.10.0

Final release before directory restructure.

- Python
Published by cgohil8 almost 2 years ago

osl-ephys - v0.9.0

What's Changed

  • The maxfilter cross talk and calibration files were moved on the hbaws computers, which caused an error. We updated maxfilter file paths to resolve this.
  • Updated cbu3_stage maxfiltering.
  • ICA labelling updates.
  • Updated batch.py, glm_epochs.py, src_report.py.
  • Installation and release notes updated.
  • Include READMEs in PyPI package. This fixes issues with installing the package using pip.

- Python
Published by cgohil8 almost 2 years ago

osl-ephys - v0.8.0

What's Changed

  • Updated TensorFlow Requirements in OSL-Dynamics by @cgohil8 in https://github.com/OHBA-analysis/osl/pull/296
  • Examples update by @cgohil8 in https://github.com/OHBA-analysis/osl/pull/297
  • Add ica input args by @matsvanes in https://github.com/OHBA-analysis/osl/pull/305
  • FEAT: oslicalabel command line function for ICA label GUI by @matsvanes in https://github.com/OHBA-analysis/osl/pull/311
  • ENH: improvement in raw and src reports. by @matsvanes in https://github.com/OHBA-analysis/osl/pull/304 and (#310) https://github.com/OHBA-analysis/osl/pull/311
  • Added the reduced HCP-MMP parcellation from L. Tait's paper. by @cgohil8 in https://github.com/OHBA-analysis/osl/pull/309
  • Updated Mac Installation by @cgohil8 in https://github.com/OHBA-analysis/osl/pull/313
  • Fixed coreg plotting on hbaws by @cgohil8 in https://github.com/OHBA-analysis/osl/pull/314

Full Changelog: https://github.com/OHBA-analysis/osl/compare/v0.7.0...v0.8.0

- Python
Published by matsvanes almost 2 years ago

osl-ephys - v0.7.0

Changes: - Parcellation demeans before PCA now. - Can read in bdf/sqd/con files. - Improved options for preprocessing/source reconstructing CTF data. - Option to pass MNI fiducials of structurals - Added functions for cleaning up headshape points and extracting fiducials/headshape points from different files (pos, elc). - Validated the function to get leadfields. - Added GLM plotting in source space. - Updated installation and instructions.

PyPI: https://pypi.org/project/osl/0.7.0/

- Python
Published by cgohil8 about 2 years ago

osl-ephys - v0.6.0

Changes: - Improvements to processing and source reconstruction functions. - Fixed bugs.

- Python
Published by cgohil8 about 2 years ago

osl-ephys - V0.5.1

No functional changes

- Python
Published by matsvanes over 2 years ago

osl-ephys - v0.5.0

The biggest change is a large enhancement of the GLM Module

- Python
Published by matsvanes over 2 years ago

osl-ephys - v0.4.0

Summary of changes: - improvements to the source recon report - changes to coregistration - fixes in maxfilter settings - fixes in preproc report

- Python
Published by matsvanes over 2 years ago

osl-ephys - v0.3.0

Substantial updates to support the 2023 OSL workshop alongside fixes and maintenance.

General summary - Addition of GLM submodule - Substantal updates to source reconstruction and parcellation - Updates for newer MNE versions - Updates to installation dependencies and conda environments

- Python
Published by AJQuinn about 3 years ago

osl-ephys - v0.2.0

General development of all subpackages, this includes: - More options and functions for source reconstruction. - Refactoring reporting: now generates a subject specific and summary report. - Fixes and additions to the batch preprocessing. - More examples scripts. - Updated installation instructions.

- Python
Published by cgohil8 over 3 years ago

osl-ephys - v0.1.1

Critical hotfix for v0.1.0 - fixes a breaking packaging error

- Python
Published by AJQuinn over 3 years ago

osl-ephys - v0.1.0

The first release of OSL in Python.

This package contains functionality for electrophysiology data processing built around MNE-Python

!! Installation is broken in v0.1.0 - use v0.1.1

- Python
Published by AJQuinn over 3 years ago