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FAQ.md
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...@@ -216,7 +216,7 @@ structure: ...@@ -216,7 +216,7 @@ structure:
1. Note that these thresholds have to be set correctly only once for each 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 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. geometry (e.g. slice tilt) between subjects shouldn't affect them significantly.
2. Setting the thresholds is an iterative procedure. You might start with the 2. Setting the thresholds is an iterative procedure. You might start with the
defaults, probably running into an error or warning (`Warning: Invalid defaults, probably running into an error or warning (`Warning: Invalid
MinPeakHeight. There are no data points greater than MinPeakHeight.` or `Not MinPeakHeight. There are no data points greater than MinPeakHeight.` or `Not
...@@ -230,11 +230,11 @@ highest peaks and most regular features reflecting slice and/or volume scan ...@@ -230,11 +230,11 @@ highest peaks and most regular features reflecting slice and/or volume scan
events. events.
4. `sync.zero` has to be smaller than `sync.slice` and `sync.vol`. It should 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 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 set this thresholds (and all other) either in absolute values or relative to the
maximum peak height. Set a value below 1, if you prefer the latter. 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 5. `sync.slice` should be about 9/10 of the typical peak height of a slice scan
event. event.
6. `sync.vol`, if you set it, should be larger than `sync.sli`. It should be 6. `sync.vol`, if you set it, should be larger than `sync.slice`. It should be
9/10 of the peak height that stands out at the beginning of a volume, and is 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 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, be, however, that there is no such peak marking the start of a volume. If so,
...@@ -247,6 +247,7 @@ onset differences. If once every few seconds (your `TR`) you find an exposed ...@@ -247,6 +247,7 @@ 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 peak, its height will give you the value for `sync.vol_spacing` (maybe reduce
it by about 5-10ms to allow for timing inaccuracies). it by about 5-10ms to allow for timing inaccuracies).
## 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`. - 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`.
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