Commit a9e19fbf authored by Lars Kasper's avatar Lars Kasper
Browse files

Release PhysIO-R2021a-v8.0.0

parent 477183c5
......@@ -4,13 +4,13 @@ RELEASE INFORMATION
Current Release
---------------
*Current version: PhysIO Toolbox Release R2020a, v7.3.0*
*Current version: PhysIO Toolbox Release R2021a, v8.0.0*
July 10th, 2020
January 29th, 2021
SCHEDULED Minor Release Notes (v7.4.0)
----------------------------------------------
SCHEDULED Minor Release Notes (v8.1.0)
--------------------------------------
### 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)
......@@ -23,11 +23,61 @@ SCHEDULED Minor Release Notes (v7.4.0)
### Fixed
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.
### Fixed
Bugfix Release Notes (v7.3.2)
-----------------------------
### Added
- version number `physio.version` in physio-struct (Gitlab issue #101)
### Fixed
- 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`
Bugfix Release Notes (v7.3.1)
-----------------------------
### Fixed
- 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
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
......
......@@ -7,4 +7,11 @@ in fMRI Data.
Journal of Neuroscience Methods 276, 56–72.
doi:10.1016/j.jneumeth.2016.10.019
If you use respiratory volume per time (RVT) regressors or preprocessing of respiratory traces, please also cite:
Harrison, S.J., Bianchi, S., Heinzle, J., Stephan, K.E., Iglesias, S., Kasper L., 2021.
A Hilbert-based method for processing respiratory timeseries.
NeuroImage, 117787. https://doi.org/10.1016/j.neuroimage.2021.117787
For a detailed snippet to be included in the methods section of your manuscript, see the FAQ in the documentation.
\ No newline at end of file
TAPAS PhysIO Toolbox
====================
*Current version: Release 2020a, v7.3.0*
*Current version: Release 2021a, v8.0.0*
> Copyright (C) 2012-2020
> Copyright (C) 2012-2021
> Lars Kasper
> <kasper@biomed.ee.ethz.ch>
>
......@@ -191,7 +191,7 @@ Features of this Toolbox
### Automatization and Performance Assessment
- Automatic creation of nuisance regressors, full integration into standard
GLMs, tested for SPM8/12 ("multiple_regressors.mat")
GLMs, tested for SPM8/12 (`multiple_regressors.mat`)
- Integration in SPM Batch Editor: GUI for parameter input, dependencies to
integrate physiological noise correction in preprocessing pipeline
- Performance Assessment: Automatic F-contrast and tSNR Map creation and display
......@@ -300,11 +300,20 @@ PhysIO Toolbox.
1. Kasper, L., Bollmann, S., Diaconescu, A.O., Hutton, C., Heinzle, J., Iglesias,
S., Hauser, T.U., Sebold, M., Manjaly, Z.-M., Pruessmann, K.P., Stephan, K.E., 2017.
The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data.
Journal of Neuroscience Methods 276, 56–72. https://doi.org/10.1016/j.jneumeth.2016.10.019
Journal of Neuroscience Methods 276, 56-72. https://doi.org/10.1016/j.jneumeth.2016.10.019
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.
### Novel methods
The following list contains references for methods originating from PhysIO
development. Please cite the relevant papers if using the techniques.
2. Harrison, S.J., Bianchi, S., Heinzle, J., Stephan, K.E., Iglesias, S., Kasper L., 2021.
A Hilbert-based method for processing respiratory timeseries.
NeuroImage, 117787. https://doi.org/10.1016/j.neuroimage.2021.117787
- *Superior RVT computation, preprocessing of respiratory traces*
### Related Papers (Implemented noise correction algorithms and optimal parameter choices)
......@@ -319,53 +328,53 @@ 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
of PhysIOlogical motion effects in fMRI: RETROICOR. Magn Reson Med 44, 162-7 (2000).
3. 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).
4. Hutton, C. et al. The impact of Physiological noise correction on fMRI at 7 T.
NeuroImage 57, 101-112 (2011).
4. Harvey, A.K. et al. Brainstem functional magnetic resonance imaging:
5. 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.
6. 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
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
7. 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,
90–101. https://doi.org/10.1016/j.neuroimage.2007.04.042
90-101. https://doi.org/10.1016/j.neuroimage.2007.04.042
#### RVT
7. Birn, R.M., Smith, M.A., Jones, T.B., Bandettini, P.A., 2008. The respiration response
function: The temporal dynamics of fMRI s ignal fluctuations related to changes in
respiration. NeuroImage 40, 644–654. doi:10.1016/j.neuroimage.2007.11.059
8. Jo, H.J., Saad, Z.S., Simmons, W.K., Milbury, L.A., Cox, R.W., 2010.
8. Birn, R.M., Smith, M.A., Jones, T.B., Bandettini, P.A., 2008. The respiration response
function: The temporal dynamics of fMRI signal fluctuations related to changes in
respiration. NeuroImage 40, 644-654. doi:10.1016/j.neuroimage.2007.11.059
9. Jo, H.J., Saad, Z.S., Simmons, W.K., Milbury, L.A., Cox, R.W., 2010.
Mapping sources of correlation in resting state FMRI, with artifact detection
and removal. NeuroImage 52, 571–582. https://doi.org/10.1016/j.neuroimage.2010.04.246
and removal. NeuroImage 52, 571-582. https://doi.org/10.1016/j.neuroimage.2010.04.246
- *regressor delay suggestions*
#### HRV
9. Chang, C., Cunningham, J.P., Glover, G.H., 2009. Influence of heart rate on the
BOLD signal: The cardiac response function. NeuroImage 44, 857–869.
10. Chang, C., Cunningham, J.P., Glover, G.H., 2009. Influence of heart rate on the
BOLD signal: The cardiac response function. NeuroImage 44, 857-869.
doi:10.1016/j.neuroimage.2008.09.029
10. Shmueli, K., van Gelderen, P., de Zwart, J.A., Horovitz, S.G., Fukunaga, M.,
11. Shmueli, K., van Gelderen, P., de Zwart, J.A., Horovitz, S.G., Fukunaga, M.,
Jansma, J.M., Duyn, J.H., 2007. Low-frequency fluctuations in the cardiac rate
as a source of variance in the resting-state fMRI BOLD signal.
NeuroImage 38, 306–320. https://doi.org/10.1016/j.neuroimage.2007.07.037
NeuroImage 38, 306-320. https://doi.org/10.1016/j.neuroimage.2007.07.037
- *regressor delay suggestions*
#### Motion (Censoring, Framewise Displacement)
11. Siegel, J.S., Power, J.D., Dubis, J.W., Vogel, A.C., Church, J.A., Schlaggar, B.L.,
12. Siegel, J.S., Power, J.D., Dubis, J.W., Vogel, A.C., Church, J.A., Schlaggar, B.L.,
Petersen, S.E., 2014. Statistical improvements in functional magnetic resonance
imaging analyses produced by censoring high-motion data points. Hum. Brain Mapp.
35, 1981–1996. https://doi.org/10.1002/hbm.22307
35, 1981-1996. https://doi.org/10.1002/hbm.22307
12. Power, J.D., Barnes, K.A., Snyder, A.Z., Schlaggar, B.L., Petersen, S.E., 2012.
13. Power, J.D., Barnes, K.A., Snyder, A.Z., Schlaggar, B.L., Petersen, S.E., 2012.
Spurious but systematic correlations in functional connectivity MRI networks
arise from subject motion. NeuroImage 59, 2142–2154.
arise from subject motion. NeuroImage 59, 2142-2154.
https://doi.org/10.1016/j.neuroimage.2011.10.018
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment