table of contents
LIPSIA     Generate a design matrix
vgendesign, vaddcovariates
The program 'vgendesign' generates a first level design matrix from a design specification (text file) by convolution with a hemodynamic modelling function. The output of this program is used by 'vcolorglm' and 'vwhiteglm' for a general linear regression. The program 'vaddcovariates' can be used to add covariates to the design matrix. The hemodynamic modelling uses the gamma function and optionally its first and second derivative. The definition of the gamma function follows Glover (1999). The user must specify the repetition time in seconds, and the number of time steps. These two specifications must agree with the experimental setup. The design matrix can be viewed using the program 'vcheckdesign'.

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.

Fixed effects analysis by concatenating design files
vgendesign -in design1.txt -out design1.v -tr 2 -ntimesteps 648 -deriv 1

vgendesign -in design2.txt -out design2.v -tr 2 -ntimesteps 648 -deriv 1

vcatdesign -in design1.v design2.v -out design.v

This sequence of program calls first generates two design matrices from two text files containing design specifications of two sessions. These two design matrices are then concatenated by 'vcatdesign' to allow for a fixed-effects analysis across sessions.

Adding covariates to the design
vaddcovariates -in design.v -out design_add.v -file covariate.txt

The call generates a new design matrix 'design_add.v' with additional columns specified by the text file 'covariate.txt'. This text file contains one or more columns whose length must correspond to the number of timesteps in the design.


Parameters of 'vgendesign ':
-help
Prints usage information.
-in
A design specification as a text file. Default: (none)
-out
Output design file. Default: (none)
-tr
Repetition time in seconds. Default: 0
-ntimesteps
Number of timesteps. Default: 0
-scanfile
ASCII file containing scan times in seconds. Default:(none)
-block
Threshold for block in seconds. Default: 10
-bkernel [ 0 | 1 ]
Type of kernel for block events (0=gauss, 1=gamma). Default: 0
-deriv [ 0 | 1 | 2 ]
Number of derivatives of the gamma function to be used for the hemodynamic modelling. Default: 1
-delay
Response delay (parameter a1). Default: 6
-undershoot
Time of undershoot (parameter a2). Default: 12
-understrength
Strength of undershoot (parameter c). Default: 0.35
-zeromean [ true | false ]
Whether to set mean of parametric covariates to zero. Default: true
Parameters of 'vaddcovariates ':
-help
Prints usage information.
-in
A design matrix generated by 'vgendesign'. Default: (none)
-out
Output design file. Default: (none)
-file
A text file containing one or more covariates as columns. Default: (none)
Literature
G.H. Glover (1999). "Deconvolution of impulse response in event-related BOLD fMRI." NeuroImage 9:416-429.


Max Planck Institute for Human Cognitive and Brain Sciences. Further Information: lipsia@cbs.mpg.de
Copyright © 2007 Max Planck Institute for Human Cognitive and Brain Sciences. All rights reserved.