table of contents
LIPSIA     Checking the design matrix
vcheckdesign
The program 'vcheckdesign' reviews a design matrix generated by the programs 'vgendesign', 'vcatdesign', 'vaddcovariates', or 'vgetcovariates'. The program 'vcheckdesign' performs a visualization of the design matrix in terms of the design and session matrix, design orthogonality, regressors, and basis functions. The regressors are visualized in the time and spectral domain.

The statistical model can be computed and visualized before fMRI data acquisition. After planning the experiment, 'vgendesign' can be executed without any fMRI data. The output is a vista-file that can be visualized using 'vcheckdesign'. If a design file (text format) is prepared, then you can call:

vgendesign -in design.des -out design.v -tr 2 -ntimesteps 648 -deriv 1

vcheckdesign -in design.v

In our example, there are 4 conditions, 648 timesteps, 2 basis functions per condition, and a repetition time of 2 s.


After calling the program, a window opens showing the design matrix. Other design properties can be viewed as follows.

Session and orthogonality matrix
Using the 'tabs' at the bottom of the window, the design matrix can be visualized in a more detailed way. If you klick onto the second tab, the session matrix can be visualized for each session. Compared with the design matrix, the session matrices are rotated by 90 degrees, thus the timeline is parallel to the horizontal axis. In our example, there is only 1 session. Using your mouse, you can get the value of the design matrix.


Klicking the third 'tab', the design orthogonality can be computed and visualized. For parameter estimation in the general linear model, the columns of the session matrices have to be orthogonal. Otherwise, the parameters are not uniquely determined. As already mentioned, the actual value of orthogonality can be obtained using the mouse. You can switch between the sessions using the menu.

Visualization of regressors in time and spectral domain
The next 2 'tabs' yield visualizations of the regressors in time and frequency domain. Klicking onto 'regressors', the regressors are visualized associated with the selected session. In our example, there are 9 columns in the only session of the design matrix. These 9 functions are visualized. For a detailed view, the middle and right mouse button can be used to zoom/unzoom the signal.


All regressors (for each session and for each condition) can be visualized in the spectral domain. Often it is helpful to see the behavior of the modelling functions in the frequency domain. For a detailed view, the middle and right mouse button can be used to zoom/unzoom the signal.


This visualisation also provides a proposal for the cutoff frequency for highpass filtering of the fMRI data. Note that the values are given in seconds. In our example, a reasonable cutoff would be 76.2 seconds or higher (largest number in the power sprectrum corresponding to an experimental condition). Note that 'vpreprocess' accepts the cutoff in seconds and not in Hz.

Visualization of the basis functions
The last 'tab' yield visualisations of the basis functions.

Parameters of 'vcheckdesign'
-help
Prints usage information.
-in
Input file. Default: (none)
-verbose [ true | false ]
Show verbose messages. Default: false


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.