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Update FAQ with info about review figures, output formats, unique features of the toolbox authored by Lars Kasper's avatar Lars Kasper
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FAQ.md
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......@@ -12,7 +12,22 @@ PhysIO stands for Physiological Input/Output toolbox, which summarizes its core
> In short, the toolbox transforms physiological input, i.e. peripheral recordings, into physiological output, i.e. regressors encoding components of physiological noise [...] A modular Matlab implementation supports command-line operation and is compatible with all major fMRI analysis packages via the export of regressor text-files. For the Statistical Parametric Mapping [SPM](<http://www.fil.ion.ucl.ac.uk/spm>) software package in particular, PhysIO features a full integration as a Batch Editor Tool, which allows user-friendly, GUI-based setup and inclusion into existing preprocessing and modeling pipelines.
2. How do I cite PhysIO?
2. How does PhysIO differ from other toolboxes for physiological noise correction for fMRI using peripheral recordings?
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Citing from the introduction of our [paper](http://dx.doi.org/10.1016/j.jneumeth.2016.10.019>): again
>
> ### Highlights ###
* A Toolbox to integrate preprocessing of physiological data and fMRI noise modeling.
* Robust preprocessing via iterative peak detection, shown for noisy data and patients.
* Flexible support of peripheral data formats and noise models (RETROICOR, RVHRCOR).
* Fully automated noise correction and performance assessment for group studies.
* Integration in fMRI pre-processing pipelines as SPM Toolbox (Batch Editor GUI).
>
3. How do I cite PhysIO?
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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)
......@@ -67,7 +82,7 @@ imaging analyses produced by censoring high-motion data points. Hum. Brain Mapp.
35, 1981–1996. doi:10.1002/hbm.22307
3. Where do I find more documentation for PhysIO?
4. Where do I find more documentation for PhysIO?
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* The paper describing its structure, objective and modules:
......@@ -79,17 +94,50 @@ imaging analyses produced by censoring high-motion data points. Hum. Brain Mapp.
* Reference Manual (for developers)
4. I am using FSL, AFNI, BrainVoyager, etc., for my fMRI Analyses. Do I need SPM for PhysIO to work?
5. I am using FSL, AFNI, BrainVoyager, etc., for my fMRI Analyses. Do I need SPM for PhysIO to work?
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No, the basic functionality of PhysIO, i.e. creating nuisance regressors for your GLM analysis, is available in plain Matlab. The following extra functionality related to automatising and assessing noise correction, require the installation of SPM:
No, the basic functionality of PhysIO, i.e. creating nuisance regressors for your GLM analysis, is available in plain Matlab. The following extra functionality related to automatizing and assessing noise correction, require the installation of SPM:
- GUI (SPM Batch Editor)
- Pipeline dependencies (automatic input of realignment parameters, feed-in of multiple regressors file to GLM)
- Model assessment via F-tests and automatic F-map/tSNR report
- Noise-ROIs model (read-in of nifti files via SPM)
5. I cannot find the answer to my question in the FAQ. Whom do I ask for help?
6. I am using device X for physiological recordings. Does PhysIO support the physiological logfile format Y?
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Currently, PhysIO natively supports the following physiological logfile types:
* General Electric
* Philips SCANPHYSLOG files (all versions from release 2.6 to 5.3)
* Siemens VB (files `.ecg', `.resp`, `.puls`
* Siemens VD (files (`*_ECG.log`, `*_RESP.log`, `*_PULS.log`)
* Biopac .mat-export
- assuming the following variables (as columns): `data`, `isi`, `isi_units`, `labels`, `start_sample`, `units`
- See `tapas_physio_read_physlogfiles_biopac_mat.m` for details
Furthermore, physiological recordings can be entered via a *custom* data format, i.e., providing one text file per device. The files should contain one amplitude value per line. The corresponding sampling interval(s) are provided as a separate parameter in the toolbox.
If your favourite logfile format is not supported, please contact the developers. We try everything to accomodate the read-in flexibility of the toolbox to your needs.
7. I am running the toolbox for a lot of subject / on a remote server without graphics. Can I somehow reproduce the output figures relevant to assess the data quality?
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Yes you can, using the toolbox function `tapas_physio_review`. This function takes the physio-structure as an input argument, which is per default saved as `physio.mat` in the specified output folder of your batch job.
8. How do I interpret the various output plots of the toolbox?
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Have a look at our publication: _The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data_ (http://dx.doi.org/10.1016/j.jneumeth.2016.10.019)
The figures there give a good overview of the toolbox output figures.
9. I cannot find the answer to my question in the FAQ. Whom do I ask for help?
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