PhysIO Toolbox Releases

GitHub_Releases CLA and Mathworks File Exchange Integration (v9.0.2)

larskasper@www.nitrc.org (Lars Kasper) — Wed, 30 Apr 2025 14:48:45 GMT

Added
--------
- Contributor License Agreement from TAPAS now also repository-specific in PhysIO

Fixed
------
- Integration with Mathworks GitHub App

## What''s Changed
* Fix physio paths and Linux/Windows cpulse mismatch by @mrikasper in https://github.com/ComputationalPsychiatry/PhysIO/pull/2

## New Contributors
* @mrikasper made their first contribution in https://github.com/ComputationalPsychiatry/PhysIO/pull/2

**Full Changelog**: https://github.com/ComputationalPsychiatry/ ... <a href="https://github.com/ComputationalPsychiatry/PhysIO/releases/tag/v9.0.2">see more</a>

GitHub_Releases Bugfix Release v9.0.1 (R2024a-v.9.0.1)

larskasper@www.nitrc.org (Lars Kasper) — Mon, 07 Apr 2025 16:41:34 GMT

Bugfix Release Notes (v9.0.1)
----------------------------

### Fixed
- Discrepancy Linux/Windows in detected cardiac pulses (`ons_secs.raw.cpulse`) for near-constant traces (e.g., in `tapas_physio_example_siemens_vb_ppu3t_sync_first_spm_job`)
due to `tapas_physio_corrcoef2` for
- Inconsistent Handling of `bids_dir`; now consistent with `save_dir` etc.: as cell in SPM job, but char in `physio` struct

GitHub_Releases PhysIO Toolbox Release R2024a, v9.0.0 (R2024a-v9.0.0)

larskasper@www.nitrc.org (Lars Kasper) — Mon, 03 Feb 2025 17:31:36 GMT

Major Release Notes (v9.0.0)
----------------------------

### Added
- BIDS writer: write out BIDS-compatbile physiological logfiles (`.tsv.gz` and `.json`)
from any vendor format
- Greatly expanded Review visualization (`tapas_physio_review`): Allow more detailed re-creation of figures from online execution, control visual verbosity retrospectively (e.g., for debugging)
- Read-In of field `AcquisitionTime` from BIDS `.json` side-car file for converted Siemens DICOMs after [dcm2niix](ht ... <a href="https://github.com/ComputationalPsychiatry/PhysIO/releases/tag/R2024a-v9.0.0">see more</a>

physio R2022a-v8.1.0

larskasper@www.nitrc.org (Lars Kasper) — Sat, 22 Jul 2023 14:47:00 GMT

Minor Release Notes (v8.1.0) ----------------------------
### Added - Compatibility of whole code base with Matlab compiler in order to run `spm_make_standalone`     - provides oppurtunity to run SPM Batch Editor GUI version of PhysIO without Matlab license requirement      - compiled version readily available within [Neurodesk](https://neurodesk.github.io/tutorials/functional_imaging/physio/)  - BIDS Read-in for separate cardiac/respiratory trace files (e.g., due to different sampling frequencies)     - see GitHub Issue #164 and pull request #167 by @alexsayal     - Additional unit tests for new read-in and example data
### Changed - Switch for certain toolbox functions (e.g., `imtool`) to only run in    non-compiled code
### Fixed - Documentation (function headers, see Github issue #149) - Typos in unused function (spotted in compilation) - Synchronization SIEMENS AcquisitionLog / Physiological files (see Github issue #172)     - better visualization of sync, clearer error messages if dummy scans not found
Bugfix Release Notes (v8.0.1) -----------------------------
### Changed - Citation of novel [TAPAS paper](https://doi.org/10.3389/fpsyt.2021.680811) in README and CITATION
 Major Release Notes (v8.0.0) ----------------------------
### Added - New method for computing respiratory volume per unit time (RVT) via the   Hilbert transform.     - Publication: Harrison et al., "A Hilbert-based method for processing       respiratory timeseries", NeuroImage, 2021.       <https://doi.org/10.1016/j.neuroimage.2021.117787>     - This is now the default option, but the old method is available by       setting `physio.model.rvt.method = ''peaks''` (or the equivalent within       the SPM batch editor).
- Respiratory preprocessing now includes an optional de-spiking step based on   median filtering.
### Changed - Now possible to change the frequencies of the respiratory filtering during   preprocessing via `physio.preproc.respiratory.filter` (or the equivalent   within the SPM batch editor).
- More robust detrending of raw respiratory timeseries via windowed padding   before filtering.

physio R2019a-v7.1.0

larskasper@www.nitrc.org (Lars Kasper) — Tue, 19 Mar 2019 8:46:00 GMT

[b]Minor Release Notes (R2019a, v7.1.0)[/b]

[b] [/b]
[b]Added[/b]
[list][*]BIDS reader and example (Brain Imaging Data Structure, http://bids.neuroimaging.io/bids_spec.pdf) for *_physio.tsv[.gz]/.json files[*]Added BioPac txt-File read-in and example[*]Template example with all physio-fields for matlab script and settings as in default SPM batch[*]Started unit testing framework in folder tests[*]example functions for findpeaks and BIDS readin[*]reference data saved with example data in subfolder TestReferenceResults[*]reference data reflects physio structure after running example scripts with PhysIO R2019a[/list]

[b]Changed[/b]
[list][*]put all functions in code into subfolders relating to different modules: readin, sync, preproc, model, assess, utils (gitlab-issue #58)[*]updated deployment tapas_physio_init because of that[*]updated figure names to reflect respective code module[*]matlab-script examples now contain more comments[*]fixed internal bug that prepended absolute paths to input logfiles in automatic example generation[*]tapas_physio_create_noise_rois_regressors with more flexible ROI reslicing options (speed-up) and uses spm_erode (no Matlab image processing toolbox needed), thanks to a contribution by Benoît Béranger[*]introduced semantic version numbers for all previous releases, and changed Release numbering to R style[*]extended documentation (FAQ, new read-in BIDS)[*]several bugfixes (Sep 18 - Mar 19), see GitHub Issues[/list]

[b]Removed[/b]
[list][*]tapas_physio_findpeaks now refers to current Matlab signal processing toolbox implementation, instead of copy of older version[*]some Matlab toolbox dependencies by custom simplified functions (e.g., suptitle)[/list]

physio PhysIO R2018.1

larskasper@www.nitrc.org (Lars Kasper) — Sat, 22 Sep 2018 22:42:00 GMT

[b]Bugfix Release Notes (R2018.1.1)[/b]
[i] [/i]

[i]Changed[/i][list][*]documentation.{html,pdf} export nicer with different FAQ numbering[/list][b]Major Release Notes (R2018.1)[/b]
[i] [/i]

[i]Added[/i][list][*]initialization function tapas_physio_init() to check Matlab paths, including SPM for batch processing[*]Extended motion diagnostics via Framewise displacement (Power et al., 2012)[*]Outlier motion models generate 'spike' regressors from FD outliers (gitlab issue #)[*]Censoring of intervals with bad physiological recordings in RETROICOR regressors (github issue #11, gitlab #36)[*]Added examples of Siemens VD (Tics Format, Prisma) and Human Connectome Project (HCP) format[/list][i]Changed[/i][list][*]Updated read-in examples of all vendors (Siemens, Philips, GE) to latest PhysIO Toolbox version.[*]Updated README.md to reflect changes to example download, new references[*]Extended Wiki documentation, in particular examples and read-in formats[/list]

physio PhysIO R2017.3

larskasper@www.nitrc.org (Lars Kasper) — Sun, 28 Jan 2018 23:17:00 GMT

[b]Minor Release Notes (R2017.3)[/b][list][*]Included references to external [ETH gitlab physio-doc repo and wiki](https://gitlab.ethz.ch/physio/physio-doc)[*]New Human Connectome Project reader for preprocessed Siemens 3-column logfiles ('*Physio_log.txt') [*]Updated Siemens Reader for Multiband patches(CMRR), versions EJA_1[*]including multi-echo data (4,5 columns)[*]multi-channel ECG data[*]significant speed up of read-in[*]generalized framework for later changes to format[*]interpolation of different sampling rates RESP/CARDIAC[*]updated README about documentation, new support policy and [TAPAS on GitHub](https://translationalneuromodeling.github.io/tapas)[*]extended FAQ[/list]

[b]Minor Release Notes (R2017.2)[/b][list][*]Included Markdown-based documentation via Wiki (also CITATION, LICENSE, CHANGELOG.md)[*]Included FAQ in Wiki[*]Split git repositories into public, dev, examples, and added wiki, to disentangle development from deployed toolbox code and data[*]Bugfix and Typo correction[*]Philips SCANPYHSLOG for their software release 5.1.7.[/list]

physio PhysIO R2017.1

larskasper@www.nitrc.org (Lars Kasper) — Wed, 08 Mar 2017 18:12:00 GMT

[b]Minor Release Notes (R2017.1)[/b][list][*]Substantially improved Siemens interface, both for VB/VD and 3T/7T releases[*]several bugfixes[*]based on extensive user feedback from Berlin and Brisbane[*]New functionality tapas_physio_overlay_contrasts.m to display non-physio[*]contrasts automatically as well[/list]
[b]Major Release Notes (r904 / R2016.1)[/b][list][*]Software version for accepted PhysIO Toolbox Paper: doi:10.1016/j.jneumeth.2016.10.019[*]Tested and expanded versions of examples[*]Improved stability by bugfixes and compatibility to Matlab R2016[*]Slice-wise regressor creation[*]Detection of constant physiological time series (detachment, clipping)[*]Refactoring of report_contrasts and compute_tsnr_gains as standalone functionality[*]Improved Read-in capabilities (Siemens respiration data, BioPac .mat)[*]Migration from svn (r904) to git (tnurepository) for version control[/list]