plot.fmridata {fmri}R Documentation

I/O functions

Description

Visualize fMRI data and (intermediate) results.

Usage

plot.fmridata(x, anatomic = NULL, maxpvalue = 0.05,
              spm = TRUE, pos = c(-1, -1, -1), type = "slice",
              device = "X11", file = "plot.png", slice =  1, view = "axial" ,zlim.u =
              NULL, zlim.o = NULL,...)

Arguments

x object of class "fmripvalue", "fmrispm" or "fmridata"
anatomic overlay of same dimension as the functional data, or fmridata object (if of x is fmripvalue object)
maxpvalue maximum p-value for thresholding
spm logical. if class is "fmrispm" decide whether to plot the t-statistics for the estimated effect (spm=TRUE) or the estimated effect itself (spm=FALSE).
pos voxel to be marked on output
type string. "slice" for slicewise view and "3d" for 3d view.
device output device if type is slice. "png", "jpeg", "ppm", default is "X11"
file name of output file if device is not "X11"
slice number of slice in x, if anatomic is of "fmridata" class
view "axial", "coronal", or "sagittal", if anatomic is of "fmridata" class
zlim.u full range for anatomical underlay used for color scale, if anatomic is of "fmridata" class
zlim.o full range for functional overlay used for color scale, if anatomic is of "fmridata" class
... additional arguments for plot

Details

Provides a sliceswise view of "fmridata" objects with anatomic overlay (if appropriate, that is for class "fmripvalue"). For objects of class "fmrispm" it plots the t-statistics for the estimated effects if spm is TRUE, or the estimated effect otherwise. For objects of class "fmridata" only a plot of the data slices itself is produced. If device is specified as "png", "jpeg", "ppm" output is done to a file. A grey/color scale is provided in the remaining space.

If type is "3d" a 3 dimensional interactive view opens. Sliders to move in the data cube are given ("x", "y", "z", and "t" if class is "fmridata" only). Time series are shown if available. For objects of class "fmrispm" a slider is created to remove information for voxels with smaller signals than a cut-off value from the plot. Use pvalues for statistical evaluation. If spm is FALSE the estimated BOLD response together with a confidence interval corresponding to maxpvalue is drawn. For objects of class "fmripvalue" the pvalues with overlay are shown.

Value

If 'type' is "3d" the Tk-object is returned. (Remove the diplay with tkdestroy(object))

Note

3 dimensional plotting requires the tkrplot package.

Author(s)

Karsten Tabelow tabelow@wias-berlin.de

See Also

fmri.pvalue

Examples

## Not run: plot(pvalue)

[Package fmri version 1.2-6 Index]