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Commit 477183c5 authored by Lars Kasper's avatar Lars Kasper

updates R2020a-v7.3.0

parent ea75f48b
RELEASE INFORMATION
===============================
===================
Current Release
---------------
*Current version: PhysIO Toolbox Release R2019b, v7.2.0*
*Current version: PhysIO Toolbox Release R2020a, v7.3.0*
August 20, 2019
July 10th, 2020
SCHEDULED Minor Release Notes (v7.4.0)
----------------------------------------------
### Added
- Brain Imaging Data Structure (BIDS) export format (`.tsv.gz`, `.json`) to save raw physiological recordings after synchronization with scanner timing (internal gitlab issue #91)
- following current BIDS specification on [continuous physiological recordings](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/06-physiological-and-other-continuous-recordings.html) and its [metadata]( https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#tabular-files)
- single tab-separated values file with columns for cardiac and respiratory recordings
- if sampling frequencies of the two differ, upsampling to higher frequency is performed
### Changed
### Fixed
Minor Release Notes (R2020a, v7.3.0)
------------------------------------
### Added
- 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
Bugfix Release Notes (v7.2.8)
-----------------------------
### Fixed
- 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
Bugfix Release Notes (v7.2.7)
-----------------------------
### Changed
- 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.
Bugfix Release Notes (v7.2.6)
-----------------------------
### Fixed
- 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
Bugfix Release Notes (v7.2.5)
-----------------------------
### Fixed
- 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
Bugfix Release Notes (v7.2.4)
-----------------------------
### Fixed
- 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 Release Notes (v7.2.3)
-----------------------------
### Fixed
- Bugfix manual peak selection (Github issue #85, Gitlab #90)
- did not work because of figure handling
Bugfix Release Notes (v7.2.2)
-----------------------------
### Fixed
- 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
Bugfix Release Notes (v7.2.1)
-----------------------------
### Changed
- PhysIO: removed Matlab statistics toolbox dependency for PCA by SVD implementation (thanks to Benoît Beranger, [pull request 64](https://github.com/translationalneuromodeling/tapas/pull/64))
- new function `tapas_physio_pca` allows for switch between stats and native SVD implementation of PCA
- comes with unit tests checking equivalency
Minor Release Notes (R2019b, v7.2.0)
......@@ -44,6 +156,7 @@ Batch Editor and Matlab-only configuration scripts. Reference data provided in
- visualization error for regressor orthogonalization (github issue #57),
when only `'RETROICOR'` set was chosen
Minor Release Notes (R2019a, v7.1.0)
------------------------------------
......
TAPAS PhysIO Toolbox
====================
*Current version: Release 2019b, v7.2.0*
*Current version: Release 2020a, v7.3.0*
> Copyright (C) 2012-2019
> Copyright (C) 2012-2020
> Lars Kasper
> <kasper@biomed.ee.ethz.ch>
>
......@@ -18,7 +18,9 @@ Download
- Please download the latest stable versions of the PhysIO Toolbox on GitHub as part of the
[TAPAS software releases of the TNU](https://github.com/translationalneuromodeling/tapas/releases).
- Older versions are available on the [TNU website](http://www.translationalneuromodeling.org/tapas).
- The latest bugfixes can be found in the [GitHub Issue Forum](https://github.com/translationalneuromodeling/tapas/issues) or by request to the authors.
- The latest bugfixes can be found in the
[development branch of TAPAS](https://github.com/translationalneuromodeling/tapas/tree/development)
and are announced in the [GitHub Issue Forum](https://github.com/translationalneuromodeling/tapas/issues).
- Changes between all versions are documented in the
[CHANGELOG](https://gitlab.ethz.ch/physio/physio-doc/blob/master/CHANGELOG.md).
......@@ -204,7 +206,7 @@ data from imperfect peripheral measures. Read-in of the following formats is
currently supported (alphabetic order):
- Biopac `.mat` and `.txt` -export
- Brain Imaging Data Structure (BIDS)
- Brain Imaging Data Structure ([BIDS](http://bids.neuroimaging.io/bids_spec.pdf) for `*_physio.tsv[.gz]/.json` files)
- Custom logfiles: should contain one amplitude value per line, one logfile per
device. Sampling interval(s) are provided as a separate parameter to the toolbox.
- General Electric
......@@ -249,15 +251,14 @@ Contributors
- Project Team:
- Steffen Bollmann, Centre for Advanced Imaging, University of Queensland, Australia
- Saskia Bollmann, Centre for Advanced Imaging, University of Queensland, Australia
- Sam Harrison, TNU Zurich
- Contributors (Code):
- Eduardo Aponte, TNU Zurich
- Tobias U. Hauser, FIL London, UK
- Sam Harrison, TNU Zurich
- Jakob Heinzle, TNU Zurich
- Chloe Hutton, FIL London, UK (previously)
- Miriam Sebold, Charite Berlin, Germany
- External TAPAS contributors listed in its [Contributor License Agreement]
(https://github.com/translationalneuromodeling/tapas/blob/master/Contributor-License-Agreement.md)
- External TAPAS contributors are listed in the [Contributor License Agreement](https://github.com/translationalneuromodeling/tapas/blob/master/Contributor-License-Agreement.md)
- Contributors (Examples):
- listed in [EXAMPLES.md](https://gitlab.ethz.ch/physio/physio-doc/wikis/EXAMPLES)
......@@ -268,7 +269,7 @@ Requirements
- All specific software requirements and their versions are in a separate file
in this folder, `requirements.txt`.
- In brief:
- PhysIO needs Matlab to run, and some of its toolboxes.
- PhysIO needs Matlab to run, and a few of its toolboxes.
- Some functionality requires SPM (GUI, nuisance regression, contrast reporting,
writing residual and SNR images).
......@@ -304,6 +305,7 @@ Journal of Neuroscience Methods 276, 56–72. https://doi.org/10.1016/j.jneumeth
The [FAQ](https://gitlab.ethz.ch/physio/physio-doc/wikis/FAQ#3-how-do-i-cite-physio)
contains a complete suggestion for a snippet in your methods section.
### Related Papers (Implemented noise correction algorithms and optimal parameter choices)
The following sections list papers that
......@@ -317,21 +319,20 @@ paper. The list is by no means complete, and we are happy to add any relevant pa
suggested to us.
#### RETROICOR
2. Glover, G.H., Li, T.Q. & Ress, D. Image‐based method for retrospective correction
2. Glover, G.H., Li, T.Q. & Ress, D. Image�based method for retrospective correction
of PhysIOlogical motion effects in fMRI: RETROICOR. Magn Reson Med 44, 162-7 (2000).
3. Hutton, C. et al. The impact of Physiological noise correction on fMRI at 7 T.
NeuroImage 57, 101‐112 (2011).
NeuroImage 57, 101�112 (2011).
4. Harvey, A.K. et al. Brainstem functional magnetic resonance imaging:
Disentangling signal from PhysIOlogical noise. Journal of Magnetic Resonance
Imaging 28, 1337‐1344 (2008).
Imaging 28, 1337�1344 (2008).
5. Bollmann, S., Puckett, A.M., Cunnington, R., Barth, M., 2018.
Serial correlations in single-subject fMRI with sub-second TR.
NeuroImage 166, 152–166. https://doi.org/10.1016/j.neuroimage.2017.10.043
#### aCompCor / Noise ROIs
6. Behzadi, Y., Restom, K., Liau, J., Liu, T.T., 2007. A component based noise
correction method (CompCor) for BOLD and perfusion based fMRI. NeuroImage 37,
......
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