Current version: PhysIO Toolbox Release R2022a, v8.1.0

April 5th, 2022

• 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
• 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

• Switch for certain toolbox functions (e.g., imtool) to only run in non-compiled code

• 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

• Citation of novel TAPAS paper in README and CITATION

• 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.

• 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.

• version number physio.version in physio-struct (Gitlab issue #101)

• Subfolder of SPM in path (fieldtrip) created ambiguous function calls to overloaded functions (Gitlab issue #102 and Gihub issue #110)
  • e.g., filtfilt in tapas_physio_filter_respiratory created flat regressors for v7.3 for Siemens VD example dataset
  • now subfolders of SPM will be removed when calling tapas_physio_main_create_regressors

• PPU read-in works for BioPac mat-file now
  • correct column labels and cardiac modality (Github Issue #103)
  • thank you to Manon Durand-Ruel @mdurandruel for reporting

• Added descriptive names for the multiple regressors matrix.
  • Closes GitLab issue #82.
  • Now possible to straightforwardly inspect physio.model.R and the contents of physio.model.output_multiple_regressors using physio.model.R_column_names.
  • Added tapas_physio_guess_regressor_names() to maintain backwards compatibility.
• New example datasets Siemens VB PPU3T with DICOM Sync (courtesy of Alexander Ritter, Jena, Germany)
• More versatile control on figure visibility, saving and closing during main and review runs of PhysIO
  • feature provided by Stephan Heunis, TU Eindhoven, The Netherlands (github issue #89)
  • figures can now be plotted in the background without disturbing interactive Matlab sessions, and can be (more) selectively saved and closed during execution of tapas_physio_review
  • more comprehensive support within tapas_physio_main_create_regressors to follow

• Bug(s) when checking SPM and PhysIO paths in tapas_physio_init under certain particular Matlab path environment settings (Gitlab merge request !37)
  • e.g., when add physio-public/code manually without subfolder
  • or if spm existed as a folder name without being added to path

• Reimplemented tapas_physio_filter_respiratory.m.
  • Closes GitLab issue #98.
  • Reduces the cut-off frequency of the high-pass filter, so as to behave more like a detrending step. Previous value of 0.1 Hz could distort e.g. sigh breaths, which can easily last upwards of 10 s.
  • Reimplements the filters themselves, with a higher filter order, extra padding, and a two step high-pass and low-pass procedure (i.e. rather than band pass) to improve the overall stability.

• Meaningful error message for auto_matched peak detection, if time series is too short
  • at least 20 peaks (and pulse templates) are required to create a pulse template
  • this is now stated explicitly, if time series is too short
  • reported by Joy Schuurmans Stekhoven, TNU, as gitlab issue #92

• Corrected documentation for preproc.cardiac.initial_cpulse_select.min parameter
  • threshold for peak relative to z-scored time series, not correlation
  • reported by Sam Harrison, TNU, as gitlab issue #95

• Stop docked figure default throwing error with -nodisplay
  • allows generating saved figure without a display, e.g., on remote server
  • bugfix provided by Sam Harrison, TNU

• Bugfix manual peak selection (Github issue #85, Gitlab #90)
  • did not work because of figure handling

• Bugfix Siemens VB (*.resp, *.puls, *.ecg)
  • Synchronization to DICOM time stamp did not work for extended physiological recordings (not starting/ending with functional run) due to ignored absolute start time stamp
  • reported by Alexander Ritter, Jena, Germany (Github issue #55, Gitlab #87)
  • probably fixes Github issue #63 (Gitlab #86) as well

• PhysIO: removed Matlab statistics toolbox dependency for PCA by SVD implementation (thanks to Benoît Beranger, pull request 64)
  • new function tapas_physio_pca allows for switch between stats and native SVD implementation of PCA
  • comes with unit tests checking equivalency

• requirements.txt making dependencies on Matlab and specific toolboxes explicit
• max_heart_rate_bpm now a user parameter to adjust prior on max allowed heart rate for cardiac pulse detection (method = 'auto_matched')
• bandpass-filtering of cardiac data during preprocessing now possible (preproc.cardiac.filter)
• Added integration tests for all examples in tests/integration for both SPM Batch Editor and Matlab-only configuration scripts. Reference data provided in examples/TestReferenceResults/examples

• Toned down and replaced irrelevant peak height and missing cardiac pulse warnings (github issue #51)
• Updated README to include external contributors and recent findings about impact of physiological noise for serial correlations (Bollmann2018)
• Added unit tests for convolution and moved all to tests/unit

• Corrected half-width shift of response functions for HRV and RVT regressors by erroneous use of Matlab conv
  • For details on the bug, its impact and fix, see our specific Release Info on RVT/HRV Bugfix
  • other references: TNU gitlab issue #83, found and fixed by Sam Harrison, TNU, see tapas_physio_conv)
• Bugfix tapas_physio_init() not working, because dependent on functions in utils subfolder not in path; utils added to path
• tapas_physio_review for motion parameters (found and fixed by Sam Harrison, TNU)
• visualization error for regressor orthogonalization (github issue #57), when only 'RETROICOR' set was chosen

• 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

• 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

• 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)

• fixed bug for matching of Philips SCANPHYSLOG-files (Gitlab #62), if physlogs were acquired on different days, but similar times

• BioPac txt-file reader (for single file, resp/cardiac/trigger data in different columns)

• fixed bug for 3D nifti array read-in in tapas_physio_create_noise_rois_regressors (github issue #24, gitlab #52)

• documentation.{html,pdf} export nicer with different FAQ numbering

• 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

• 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

• Included references to external ETH gitlab physio-doc repo and wiki
• 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
• extended FAQ

• 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.

• 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

• 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

• Software version for Toolbox Paper submission
• Noise ROIs modeling
• Extended motion models (24 parameters, Volterra expansion)
• HRV/RVT models with optional multiple delay regressors
• Report_contrasts with automatic contrast generation for all regressor groups
• compute_tsnr_gains for individual physiological regressor groups
• consistent module naming (scan_timing, preproc)
• Visualisation improvement (color schemes, legends)

• Compatibility tested for SPM12, small bugfixes Batch Dependencies
• Cleaner Batch Interface with grouped sub-menus (cfg_choice)
• new model: 'none' to just read out physiological raw data and preprocess, without noise modelling
• Philips: Scan-timing via gradient log now automatized (gradient_log_auto)
• Siemens: Tics-Logfile read-in (proprietary, needs Siemens-agreement)
• All peak detections (cardiac/respiratory) now via auto_matched algorithm
• Adapt plots/saving for Matlab R2014b

• Read-in of Siemens plain text log files; new example dataset for Siemens
• Speed up and debugging of auto-detection method for noisy cardiac data => new method thresh.cardiac.initial_cpulse_select.method = 'auto_matched'
• Error handling for temporary breathing belt failures (Eduardo Aponte, TNU Zurich)
• slice-wise regressors can be created by setting sqpar.onset_slice to a index vector of slices

• SPM matlabbatch GUI implemented (Call via Batch -> SPM -> Tools -> TAPAS PhysIO Toolbox)
• improved, automatic heartbeat detection for noisy ECG now standard for ECG and Pulse oximetry (courtesy of Steffen Bollmann)
• QuickStart-Manual and PhysIO-Background presentation expanded/updated
• job .m/.mat-files created for all example datasets
• bugfixes cpulse-initial-select method-handling (auto/manual/load)

• Cardiac and Respiratory response function regressors integrated in workflow (heart rate and breathing volume computation)
• Handling of Cardiac and Respiratory Logfiles only
• expanded documentation (Quickstart.pdf and Handbook.pdf)
• read-in of custom log files, e.g. for BrainVoyager peripheral data
• more informative plots and commenting (especially in tapas_physio_new).

• computation of heart and breathing rate in Philips/PPU/main_PPU.m
• prefix of functions with tapas_*

• complete modularization of reading/preprocessing/regressor creation for peripheral physiological data
• manual selection of missed heartbeats in ECG/pulse oximetry (courtesy of Jakob Heinzle)
• support for logfiles from GE scanners (courtesy of Steffen Bollmann, KiSpi Zuerich)
• improved detection of pulse oximetry peaks (courtesy of Steffen Bollmann)
• improved documentation
• consistent function names (prefixed by "physio_")

NOTE: Your main_ECG/PPU.m etc. scripts from previous versions (<=r159) will not work with this one any more. Please adapt one of the example scripts for your needs (~5 min of work). The main benefit of this version is a complete new variable structure that is more sustainable and makes the code more readable.