Table 1 

The parameters of the function TEprepare.m 

field name of cfg. 
default 
input 
description 


sgncmb 
strings 
Nx2 cell array of specific channel pairs to analyze 



channel 
strings 
cell array of channel names, all combinations will be tested 



Path2TSTOOL 
string 
path to the folder including the required TSTOOL package 



toi 
vector 
first and last time point of the time range of interest (in seconds) 



predictiontime_u 
integer number 
estimated prediction time (in milliseconds) 



optimizemethod 
string 
Method to optimize parameters: 'ragwitz' or 'cao' 



ragdim 
1 to 10 
vector 
In case of optimizemethod = 'ragwitz': range of embedding dimensions to scan 


ragtaurange 
vector 
In case of optimizemethod = 'ragwitz': 1 × 2 vector of min and max embedding delays (in units of ACT) 



ragtausteps 
10 
integer number 
In case of optimizemethod = 'ragwitz': number of equidistant steps in ragtaurange (minimum 5) 


flagNei 
string 
In case of optimizemethod = 'ragwitz': 'Range' or 'Mass' type of neighbor search 



sizeNei 
integer number 
In case of optimizemethod = 'ragwitz': Radius or mass for the neighbor search according to flagNei 



repPred 
integer number 
In case of optimizemethod = 'ragwitz': repPred represents the number of sample points for which the prediction is performed (it has to be smaller than length(timeSeries)  (d  1) * tau * ACT  u) 



caodim 
1 to 10 
integer number 
In case of optimizemethod = 'cao': indicates the range of embedding dimensions d that is scanned using the Cao criterion to find the optimal dimension 


caokth_neighbors 
4 
integer number 
In case of optimizemethod = 'cao': number of neighbors for fixed mass search for cao (controls balance of bias/statistical errors) 


tau 
1.5 
number 
In case of optimizemethod = 'cao': embedding delay (in units of ACT) 


kth_neighbors 
4 
integer number 
number of neighbors for fixed mass search in TE calculation (controls balance of bias/statistical errors). In case of using optimizemethod = 'cao': kth_neighbors = caokth_neighbors 


TheilerT 
'ACT' 
integer number or 'ACT' 
number of temporal neighbors excluded to avoid serial correlations in TE calculation (Theiler correction) 


trialselect 
'ACT' 
string 
selecting trials: 'no' = use all trials, 'range' = use range of trial numbers, 'ACT' use trials with ACT lower than threshold 


actthrvalue 
integer number 
in case of trialselect='ACT' maximum threshold of the ACT for trial selection 



trial_from 
integer number 
first trial in case of range selection of trials 



trial_to 
integer number 
last trial in case of range selection of trials 



maxlag 
1000 
integer number 
the range of lags for computing the ACT: from MAXLAG to MAXLAG (in samples) 


This table contains all possible parameters for the configuration structure cfg of the function TEprepare.m (TRENTOOL Version 1.0) For integer numbers no type casting has to be performed! 

Lindner et al. BMC Neuroscience 2011 12:119 doi:10.1186/1471220212119 