TCIU (version 1.2.7)

fmri_3dvisual: visualization of the 3D brain with the activated areas

Description

a visualization method, using plotly to draw the 3D plot of the brain with the activated areas determined by p-values, which is generated from fMRI data

Usage

fmri_3dvisual(
  pval,
  mask,
  p_threshold = 0.05,
  method = "scale_p",
  color_pal = "YlOrRd",
  multi_pranges = TRUE,
  title = NULL
)

Value

a list of two elements

• plot - the 3d plot of the fMRI data drawn by plotly

• pval_df - data.frame with the p value for each voxel and the specified color for it

Arguments

pval

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

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.

method

a string that represents method for the plot. There are 2 options: 'scale_p' and 'low5_percent'. The default is 'scale_p'. '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.

title

the title of the plot. The default is NULL.

Author

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

Details

The function fmri_3dvisual is used to visualize the 3D plot of the brain with its activated parts based on provided p values. The p values are generated by applying statistical test on fMRI data. When providing input of a 3D p-values data, a 3D interactive plot will be generated with surface for the brain shell and scatter points in different colors and size representing different stimulated levels.

Examples

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

# make the 3D plot
fmri_3dvisual(phase2_pval, mask, p_threshold = 0.05, method="scale_p")$plot