plot.fmridata: 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",...)

Arguments

object of class "fmripvalue", "fmrispm" or "fmridata"

anatomic

overlay of same dimension as the functional data

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"

...

additional arguments for plot

Value

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

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 TRUE 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.

Examples

Run this code

plot(pvalue)