The design specification of first level designs must be given as a text file
as specified in 'designformat'.
Example:
vgendesign -in design.txt -out design.v -tr 2 -ntimesteps 648 -deriv 2
This program call generates a design matrix 'design.v' from the specification file 'design.txt'.
The TR is 2 seconds, and there are 648 timesteps.
The hemodynamic modelling is done using a gamma function and its first and second derivative ('-deriv 2').
The parameters (a1,a2,c) of the gamma function can be modified using the parameters '-delay', '-undershoot', '-understrength'.
If the interscan intervals (repetition times) are not constant,
then an ASCII text file must be supplied. Each line in this file must
contain the scan time in seconds for each scan. The parameter
'-scanfile' is used to specify this file.
Normally, the gamma function as introduced by Glover (1997) is used for hemodynamic modelling.
However, for block designs, a Gaussian or modified Gamma function are
often better
suited. The parameter '-block' can be used to switch from specifies
blocks of stimuli. This parameter has to be given in seconds. Every
event type with a mean duration exceeding this value will be treated as
'block'. Event event type with mean duration below this time is
modelled as 'event'.
Example:
vgendesign -in design.txt -out
design.v -tr 2 -ntimesteps 648 -deriv 2 -block 10
This call is almost identical to the example above, except that event
types with a mean duration longer than 10 seconds will be modelled as
blocks and convolved with a Gaussian.