TCIU (version 1.2.7)

fmri_2dvisual: visualization of the 2D brain (axial, sagittal and coronal) with the activated areas

Description

a visualization method, using ggplot2 to draw the brain from axial, sagittal and coronal view with activated area identified by p-values

Usage

fmri_2dvisual(
  pval,
  axis_ls,
  hemody_data = NULL,
  mask,
  p_threshold = 0.05,
  legend_show = TRUE,
  method = "scale_p",
  color_pal = "YlOrRd",
  multi_pranges = TRUE,
  mask_width = 1.5
)

Value

a plot drawn by ggplot2

Arguments

pval

a 3D array of p-values used to plot activated area of the brain

axis_ls

a list with two elements. The first element is the character of 'x', 'y', 'z'. The second element is an integer showing a specific slice on the fixed axis identified in the first element.

hemody_data

a parameter to have the plot with/without hemodynamic contour. The default is NULL to make the plot without hemodynamic contour, otherwise assign a 3D array of the hemodynamic data.

mask

a 3D nifti or 3D array of data to show the shell of the brain

p_threshold

NULL or a numeric value that can be selected randomly below 0.05 to drop all p-values above the threshold. If 'low5_percent' method is used, make 'p_threshold' as NULL. The default is 0.05.

legend_show

a logical parameter to specify whether the final plot has legend

method

a string that represents method for the plot. There are 3 options: 'min_max', 'scale_p' and 'low5_percent'. The default is 'scale_p'. 'min_max' is to draw plot based on the color scale of the minimum and maximum of the p value; 'scale_p' is to draw the plot with fixed color scale for fixed range of p value; 'low5_percent' is to draw the plot for the smallest 5 percent of p value when all the p values are not significant.

color_pal

the name of the color palettes provided by RColorBrewer. The default is "YlOrRd".

multi_pranges

an option under 'scale_p' method to decide whether there are at most 9 colors in the legend for the ranges of p value, or at most 4 colors. The default is TRUE, choosing the larger number of colors for the plot.

mask_width

a numeric value to specify the width of mask contour. The default is 1.5.

Author

SOCR team <http://socr.umich.edu/people/>

Details

The function fmri_2dvisual is used to find activated part of the brain based on given p values from sagittal, axial and coronal view. When providing input of the p-values, the specific plane and index to slice on, the mask data and the hemodynamic data of the brain, a plot will be generated with the heat map for the activated parts, the black contour showing the position of the brain, and the blue contour representing the hemodynamic contour.

Examples

# sample 3D data of mask provided by the package
dim(mask)
# sample 3D p value provided by the package
dim(phase2_pval)

# plot the sagittal, coronal and axial view of this p value generated from the brain fMRI data
# \donttest{
fmri_2dvisual(phase2_pval, list('x',40), hemody_data=NULL, mask=mask, p_threshold=0.05)
# }