Changes

- changed formatting of question titles to ## for better display online
Lars Kasper · fcc5fb29
--- a/FAQ.md
+++ b/FAQ.md
@@ -2,8 +2,7 @@ Frequently Asked Questions (FAQ)
 ================================


-1) What is the PhysIO Toolbox?
------------------------------
+## 1. What is the PhysIO Toolbox?

 PhysIO is a toolbox for model-based physiological noise correction of fMRI data.

@@ -13,8 +12,7 @@ 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 does PhysIO differ from other toolboxes for physiological noise correction for fMRI using peripheral recordings?
-----------------------------------------------------------------------------------------------------------------------
+## 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 

@@ -28,8 +26,7 @@ Citing from the introduction of our [paper](http://dx.doi.org/10.1016/j.jneumeth
 >


-3) How do I cite PhysIO?
------------------------
+## 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)

@@ -80,8 +77,7 @@ imaging analyses produced by censoring high-motion data points. Hum. Brain Mapp.
 35, 1981–1996. doi:10.1002/hbm.22307


-4) Where do I find more documentation for PhysIO?
-------------------------------------------------
+## 4. Where do I find more documentation for PhysIO?

 * The [paper](http://dx.doi.org/10.1016/j.jneumeth.2016.10.019) describing its structure, objective and modules
 * [README.md](https://gitlab.ethz.ch/physio/physio-doc/blob/master/README.md) in the main folder when downloading
@@ -92,8 +88,7 @@ imaging analyses produced by censoring high-motion data points. Hum. Brain Mapp.
 * Reference Manual (for developers)


-5) 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?

 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:

@@ -103,8 +98,7 @@ No, the basic functionality of PhysIO, i.e. creating nuisance regressors for you
 - Noise-ROIs model (read-in of nifti files via SPM)


-6) I am using device X for physiological recordings. Does PhysIO support the physiological logfile format Y?
------------------------------------------------------------------------------------------------------------
+## 6. I am using device X for physiological recordings. Does PhysIO support the physiological logfile format Y?

 Currently, PhysIO natively supports the following physiological logfile types:

@@ -114,23 +108,25 @@ Currently, PhysIO natively supports the following physiological logfile types:
 - Siemens VD/VE (files `*_ECG.log`, `*_RESP.log`, `*_PULS.log`)
    - including CMRR-derived multiband-files
 - Siemens Human Connectome Project log files (preprocessed 3 column files `*_Physio_log.txt`)
- Biopac .mat-export
+- 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
+- Biopac `.txt`-export
+    - assuming the following 4 columns, with one sample per row: respiratory, skin conductance (GSR),  cardiac (PPG), and trigger signal (on/off)
+    
+See [Read-In of Logfiles](MANUAL_PART_READIN) for a detailed description of the expected file formats.

 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 subjects / on a remote server without graphics. Can I somehow reproduce the output figures relevant to assess the data quality?
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## 7. I am running the toolbox for a lot of subjects / on a remote server without graphics. Can I somehow reproduce the output figures relevant to assess the data quality?

 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?
--------------------------------------------------------------
+## 8. How do I interpret the various output plots of the toolbox?

 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)

@@ -141,8 +137,7 @@ The figures there give a good overview of the toolbox output figures, in particu
 - Fig. 9: Group results/typical activation sites for F-contrasts of RETROICOR regressors (cardiac/resp/interaction)


-9) I want to access subject's physiological measures, e.g. heart rate or respiratory volume (per time), before they enter the regressors. Where can I do that?
--------------------------------------------------------------------------------------------------------------------------------------------------------------
+## 9. I want to access subject's physiological measures, e.g. heart rate or respiratory volume (per time), before they enter the regressors. Where can I do that?

 All intermediate data processing steps (e.g. filtering, cropping) of the peripheral data, including the computation of physiologically meaningful time courses, such as heart rate and respiratory volume, are saved in the substructure `ons_secs` ("onsets in seconds) of the physio-structure mentioned in question 7. This structure is typically saved in a file `physio.mat`.

@@ -164,8 +159,7 @@ All intermediate data processing steps (e.g. filtering, cropping) of the periphe
 For a detailed list of all properties and their documentation, read the source code of `tapas_physio_new.m`


-10) What is the order of the regressor columns in the multiple regressors file?
-------------------------------------------------------------------------------
+## 10. What is the order of the regressor columns in the multiple regressors file?

 This depends on the physiological models (and their order) specified in the `model`-submodule of physio (or in the batch editor). The general order is outlined in Fig. 7A of the  [Main PhysIO Toolbox Paper](http://dx.doi.org/10.1016/j.jneumeth.2016.10.019). The []-brackets indicate the number of regressors:

@@ -181,8 +175,7 @@ This depends on the physiological models (and their order) specified in the `mod
 If any of the models was not specified, the number of regressors is reduced accordingly.


-11) How do I know whether the physiological noise correction worked?
--------------------------------------------------------------------
+## 11. How do I know whether the physiological noise correction worked?

 The best way to assess the quality of the correction is an F-test over the respective physiological noise model regressors in the design matrix. Luckily, if you use SPM, the toolbox can create these contrasts and corresponding output plots with overlays of your brain automatically via calling the following function in the Matlab command window:

@@ -203,8 +196,7 @@ If your F-contrast results differ or are absent, have a look at the *Diagnostic
 Other than that, scan timing synchronisation is a major source of error, so always check the *Cutout actual scans* plot, whether the curves and scan events, TR etc. make sense.


-12) Philips: I would like to use the gradient log for timing synchronization, but how do I set the thresholds?
--------------------------------------------------------------------------------------------------------------
+## 12. Philips: I would like to use the gradient log for timing synchronization, but how do I set the thresholds?

 Have a look at the following figure:

@@ -213,16 +205,14 @@ Have a look at the following figure:
 This figure can be found as [figure S1](https://www.sciencedirect.com/science/article/pii/S016502701630259X#sec0125) in the supplementary material of our [paper](https://doi.org/10.1016/j.jneumeth.2016.10.019).


-13) How do I know which logfile type ('vendor') I have to choose?
-----------------------------------------------------------------
+## 13. How do I know which logfile type ('vendor') I have to choose?

 - Typically, you will know your scanner manufacturer or the supplier of your peripheral recording device. The currently supported vendors can always be found in the SPM Batch Editor, as dropdown options for the vendor parameter in any PhysIO batch, and are also listed as cases in `tapas_physio_read_physlogfiles.m`.
 - For Siemens, since there are a couple of formats, it is often helpful to check the extensions of the files (or the file name structure in general) see question 7.
 - Sometimes you will have to look in the log files themselves and compare them to the examples provided on the [Data Section](https://www.tnu.ethz.ch/en/software/tapas/data.html) of our homepage.


-14) What does Parameter *XY* mean and what is its best setting?
---------------------------------------------------------------
+## 14. What does Parameter *XY* mean and what is its best setting?

 Before you ask us directly, there are two simple ways to find out more about the parameters and options of the PhysIO toolbox:

@@ -230,8 +220,7 @@ Before you ask us directly, there are two simple ways to find out more about the
 - Within Matlab, type `edit tapas_physio_new`. This constructor function lists all parameters of the physio-structure with inline comments on their purpose and possible values.


-15) I cannot find the answer to my question in the FAQ. Whom do I ask for help?
-------------------------------------------------------------------------------
+## 15. I cannot find the answer to my question in the FAQ. Whom do I ask for help?

 We are very happy to provide support on how to use the PhysIO Toolbox. However, 
 as every researcher, we only have a limited amount of time. So please excuse, if