fmri: Analysis of fMRI Experiments

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Visualize fMRI data and (intermediate) results.

## S3 method for class 'fmridata'
plot(x, anatomic = NULL, maxpvalue = 0.05,
              spm = TRUE, pos = c(-1, -1, -1), type = "slice",
              slice =  1, view = "axial" ,zlim.u =
              NULL, zlim.o = NULL,col.o = heat.colors(256), col.u =
              grey(0:255/255), cutOff = c(0, 1), ...)
## S3 method for class 'fmrisegment'
plot(x, anatomic = NULL,
              slice =  1, view = c( "axial", "coronal", "sagittal") ,zlim.u =
              NULL, zlim.o = NULL,col.o = c( rainbow( 64, start = 2/6, end = 4/6),
              rainbow( 64, start = 0, end = 1/6)),
              col.u = grey(0:127/127), verbose = FALSE, ...)

`x`	object of class "fmrisegment", "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.
`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
`col.u`	color scale for anatomical underlay, if anatomic is of "fmridata" class, default grey(0:255/255)
`col.o`	color scale for functional overlay, if anatomic is of "fmridata" class, default heat.colors(256)
`cutOff`	not yet documented
`verbose`	tell something on the progress?
`...`	additional arguments for plot

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.

For objects of class "fmrisegment" the smoothed signal size is shown in the activation segments (two-sided test!).

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.

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

3 dimensional plotting requires the tkrplot package.

Karsten Tabelow tabelow@wias-berlin.de

Polzehl, J. and Tabelow, K. (2007) fmri: A Package for Analyzing fmri Data, R News, 7:13-17 .

fmri.pvalue