FAQ.md

@@ -204,6 +204,40 @@ 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).
 
+The following heuristics might help with the `sync` settings:
+
+1. Note that these thresholds have to be set correctly only once for each
+functional sequence, i.e., usually once per study. Even small changes to scan
+geometry (e.g. slice tilt) between subject shouldn't affect them significantly.
+2. Setting the thresholds is an iterative procedure. You might start with the
+defaults, probably running into an error or warning (`Warning: Invalid
+  MinPeakHeight. There are no data points greater than MinPeakHeight.` or `Not
+  enough volume/slice scan events found`). Then you inspect the figure output
+  resembling the one above and adjust (usually lower) the thresholds in the
+  order mentioned below.
+3. There are three time courses in the upper of the three subplots shown in the
+figure. These time courses show the traces of the three gradient directions
+`x`,`y`,`z`. Choose the one as `sync.grad_direction` parameter that has the
+highest peaks and most regular features reflecting slice and/or volume scan
+events.
+4. `sync.zero` has to be smaller than `sync.slice` and `sync.vol`. It should
+be about 4/5 of the typical peak height in the gradient trace. Note that you can
+set this syncolds (and all other) either in absolute values or relative to the
+maximum peak height. Set a value below 1, if you prefer the latter.
+5. `sync.sli` should be about 9/10 of the typical peak height of a slice scan
+event.
+6. `sync.vol`, if you set it, should be larger than `sync.sli`. It should be
+9/10 of the peak height that stands out at the beginning of a volume, and is
+followed by some dozens of smaller peaks (for the slices) typically. It might
+be, however, that there is no such peak marking the start of a volume. If so,
+you might try `sync.vol_spacing` or leave it empty and rely on the slice
+thresholds exclusively
+6. `sync.vol_spacing`, if set, should reflect the temporal spacing (in seconds),
+between the end of the previous volume and the start of the next one. The figure
+above gives some idea how to do that based on the bottom subplot that shows peak
+onset differences. If once every few seconds (your `TR`) you find an exposed
+peak, its height will give you the value for `sync.vol_spacing` (maybe reduce
+it by about 5-10ms to allow for timing inaccuracies).
 
 ## 13. How do I know which logfile type ('vendor') I have to choose?