| ... | ... | @@ -15,7 +15,7 @@ PhysIO stands for Physiological Input/Output toolbox, which summarizes its core |
|
|
|
2. How does PhysIO differ from other toolboxes for physiological noise correction for fMRI using peripheral recordings?
|
|
|
|
----------------------------------------------------------------------------------------------------------------------
|
|
|
|
|
|
|
|
Citing from the introduction of our [paper](http://dx.doi.org/10.1016/j.jneumeth.2016.10.019>): again
|
|
|
|
Citing from the introduction of our [paper](http://dx.doi.org/10.1016/j.jneumeth.2016.10.019>) again
|
|
|
|
|
|
|
|
>
|
|
|
|
> ### Highlights ###
|
| ... | ... | @@ -30,18 +30,18 @@ Citing from the introduction of our [paper](http://dx.doi.org/10.1016/j.jneumeth |
|
|
|
3. How do I cite PhysIO?
|
|
|
|
------------------------
|
|
|
|
|
|
|
|
The core reference for PhysIO is: _The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data_ (http://dx.doi.org/10.1016/j.jneumeth.2016.10.019)
|
|
|
|
The **core reference for PhysIO** is: _The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data_ (http://dx.doi.org/10.1016/j.jneumeth.2016.10.019)
|
|
|
|
|
|
|
|
Please cite this paper if you use PhysIO in your work. Moreover, this paper is also a good source for more information on PhysIO (see next question).
|
|
|
|
|
|
|
|
A standard snippet to include in your method section could look like the following, assuming you use our specific implementation of RETROICOR, which uses Fourier expansions of different order for the estimated phases of cardiac pulsation (3rd order), respiration (4th order) and cardio-‐respiratory interactions (1st order) following (Harvey et al., 2008)
|
|
|
|
A **standard snippet to include** in your method section could look like the following, assuming you use our specific implementation of RETROICOR, which uses Fourier expansions of different order for the estimated phases of cardiac pulsation (3rd order), respiration (4th order) and cardio-‐respiratory interactions (1st order) following (Harvey et al., 2008)
|
|
|
|
|
|
|
|
> Correction for physiological noise was performed via RETROICOR [1,2] using Fourier
|
|
|
|
> expansions of different order for the estimated phases of cardiac pulsation (3rd order),
|
|
|
|
> respiration (4th order) and cardio-‐respiratory interactions (1st order) [2]: The
|
|
|
|
> corresponding confound regressors were created using the Matlab PhysIO Toolbox ([4],
|
|
|
|
> open source code available as part of the TAPAS software collection:
|
|
|
|
> https://www.tnu.ethz.ch/en/software/tapas.html).
|
|
|
|
> https://www.translationalneuromodeling.org/tapas).
|
|
|
|
|
|
|
|
1. 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-‐
|
| ... | ... | @@ -54,13 +54,10 @@ NeuroImage 57, 101-‐112 (2011). |
|
|
|
Disentangling signal from PhysIOlogical noise. Journal of Magnetic Resonance
|
|
|
|
Imaging 28, 1337-‐1344 (2008).
|
|
|
|
|
|
|
|
4. 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., 2016.
|
|
|
|
The PhysIO Toolbox for Modeling PhysIOlogical Noise in fMRI Data. Journal of
|
|
|
|
Neuroscience Methods accepted. doi:10.1016/j.jneumeth.2016.10.019
|
|
|
|
4. 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. doi:10.1016/j.jneumeth.2016.10.019
|
|
|
|
|
|
|
|
If you use respiratory‐volume-per time (RVT), heart-‐rate
|
|
|
|
variability (HRV), noise ROIs or 12/24 regressor motion modeling, also include the
|
|
|
|
If you use **respiratory‐volume-per time (RVT), heart-‐rate
|
|
|
|
variability (HRV), noise ROIs or 12/24 regressor motion modeling**, also include the
|
|
|
|
respective references:
|
|
|
|
|
|
|
|
5. Behzadi, Y., Restom, K., Liau, J., Liu, T.T., 2007. A component based noise
|
| ... | ... | @@ -85,8 +82,8 @@ imaging analyses produced by censoring high-motion data points. Hum. Brain Mapp. |
|
|
|
4. Where do I find more documentation for PhysIO?
|
|
|
|
-------------------------------------------------
|
|
|
|
|
|
|
|
* The paper describing its structure, objective and modules:
|
|
|
|
* README.md in the main folder when downloading
|
|
|
|
* The [paper](http://dx.doi.org/10.1016/j.jneumeth.2016.10.019) describing its structure, objective and modules
|
|
|
|
* [README.md](https://tnurepository.ethz.ch/physio/physio-public/blob/master/README.md) in the main folder when downloading
|
|
|
|
- For help on installation and getting started
|
|
|
|
* Quickstart
|
|
|
|
- PDF (or markdown .md file)
|
| ... | ... | |
