Commit 02ea9e32 authored by Lars Kasper's avatar Lars Kasper
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v8.0.1

parent a9e19fbf
......@@ -4,9 +4,9 @@ RELEASE INFORMATION
Current Release
---------------
*Current version: PhysIO Toolbox Release R2021a, v8.0.0*
*Current version: PhysIO Toolbox Release R2021a, v8.0.1*
January 29th, 2021
June 16th, 2021
SCHEDULED Minor Release Notes (v8.1.0)
......@@ -23,6 +23,13 @@ SCHEDULED Minor Release Notes (v8.1.0)
### Fixed
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)
----------------------------
......
......@@ -7,6 +7,18 @@ in fMRI Data.
Journal of Neuroscience Methods 276, 56–72.
doi:10.1016/j.jneumeth.2016.10.019
Please also cite the parent software collection TAPAS:
Frässle, S., Aponte, E.A., Bollmann, S., Brodersen, K.H., Do, C.T., Harrison, O.K.,
Harrison, S.J., Heinzle, J., Iglesias, S., Kasper, L., Lomakina, E.I., Mathys, C.,
Müller-Schrader, M., Pereira, I., Petzschner, F.H., Raman, S., Schöbi, D.,
Toussaint, B., Weber, L.A., Yao, Y., Stephan, K.E., 2021.
TAPAS: an open-source software package for Translational Neuromodeling and Computational Psychiatry.
Frontiers in Psychiatry 12, 857.
https://doi.org/10.3389/fpsyt.2021.680811
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.
......@@ -14,4 +26,4 @@ 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
For a detailed snippet to be included in the methods section of your manuscript, see the FAQ in the documentation.
TAPAS PhysIO Toolbox
====================
*Current version: Release 2021a, v8.0.0*
*Current version: Release 2021a, v8.0.1*
> Copyright (C) 2012-2021
> Lars Kasper
......@@ -289,31 +289,41 @@ open source projects and gratefully acknowledges their use.
- Matlab file exchange, adam.tudorjones@pharm.ox.ac.uk
References
----------
Cite Me
-------
### Main Toolbox Reference
### Main Toolbox and TAPAS Reference
Please cite the following paper in all of your publications that utilized the
Please cite the following papers in all of your publications that utilized the
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
- *main PhysIO Toolbox reference*
2. Frässle, S., Aponte, E.A., Bollmann, S., Brodersen, K.H., Do, C.T., Harrison, O.K., Harrison, S.J., Heinzle, J., Iglesias, S., Kasper, L., Lomakina, E.I., Mathys, C., Müller-Schrader, M., Pereira, I., Petzschner, F.H., Raman, S., Schöbi, D., Toussaint, B., Weber, L.A., Yao, Y., Stephan, K.E., 2021. TAPAS: an open-source software package for Translational Neuromodeling and Computational Psychiatry. Frontiers in Psychiatry 12, 857. https://doi.org/10.3389/fpsyt.2021.680811
- *main TAPAS software collection reference*
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.
You can include the following snippet in your Methods section,
along with a brief description of the physiological noise models used:
### Novel methods
> The analysis was performed using the Matlab PhysIO Toolbox ([1], version x.y.z,
> open-source code available as part of the TAPAS software collection: [2],
> <https://www.translationalneuromodeling.org/tapas>)
The following list contains references for methods originating from PhysIO
development. Please cite the relevant papers if using the techniques.
If you use respiratory volume per time (RVT) regressors or preprocess respiratory traces
for RETROICOR, please also cite:
2. Harrison, S.J., Bianchi, S., Heinzle, J., Stephan, K.E., Iglesias, S., Kasper L., 2021.
3. 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*
- *superior RVT computation, preprocessing of respiratory traces*
Our [FAQ](https://gitlab.ethz.ch/physio/physio-doc/wikis/FAQ#3-how-do-i-cite-physio)
contains a suggestion for a more comprehensive RETROICOR-related methods paragraph.
See the [main TAPAS README](../README.md) for more details on citing TAPAS itself.
### Related Papers (Implemented noise correction algorithms and optimal parameter choices)
......@@ -328,51 +338,51 @@ paper. The list is by no means complete, and we are happy to add any relevant pa
suggested to us.
#### RETROICOR
3. Glover, G.H., Li, T.Q. & Ress, D. Image-based method for retrospective correction
4. 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).
4. Hutton, C. et al. The impact of Physiological noise correction on fMRI at 7 T.
5. Hutton, C. et al. The impact of Physiological noise correction on fMRI at 7 T.
NeuroImage 57, 101-112 (2011).
5. Harvey, A.K. et al. Brainstem functional magnetic resonance imaging:
6. Harvey, A.K. et al. Brainstem functional magnetic resonance imaging:
Disentangling signal from PhysIOlogical noise. Journal of Magnetic Resonance
Imaging 28, 1337-1344 (2008).
6. Bollmann, S., Puckett, A.M., Cunnington, R., Barth, M., 2018.
7. 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
7. Behzadi, Y., Restom, K., Liau, J., Liu, T.T., 2007. A component based noise
8. 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
#### RVT
8. Birn, R.M., Smith, M.A., Jones, T.B., Bandettini, P.A., 2008. The respiration response
9. 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.
10. 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
- *regressor delay suggestions*
#### HRV
10. Chang, C., Cunningham, J.P., Glover, G.H., 2009. Influence of heart rate on the
11. 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
11. Shmueli, K., van Gelderen, P., de Zwart, J.A., Horovitz, S.G., Fukunaga, M.,
12. 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
- *regressor delay suggestions*
#### Motion (Censoring, Framewise Displacement)
12. Siegel, J.S., Power, J.D., Dubis, J.W., Vogel, A.C., Church, J.A., Schlaggar, B.L.,
13. 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
13. Power, J.D., Barnes, K.A., Snyder, A.Z., Schlaggar, B.L., Petersen, S.E., 2012.
14. 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.
https://doi.org/10.1016/j.neuroimage.2011.10.018
......
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