TCIU (version 1.2.7)

fmri_3dvisual_region: visualization of the 3D brain with the activated areas by regions

Description

an improved visualization method of fmri_3dvisual, using plotly to draw the 3D plot of the brain with the activated areas region by region

Usage

fmri_3dvisual_region(
  pval,
  mask,
  label_index,
  label_name,
  top_num = NULL,
  p_threshold = 0.05,
  method = "scale_p",
  multi_pranges = TRUE,
  color_pal = "YlOrRd",
  rank = NULL,
  title = NULL
)

Value

the 3d plot of the fMRI data drawn by plotly

Arguments

pval

a 3D or 1D or a list of two 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 regions of the brain

label_index

a 1D array listing the label number in the mask

label_name

a 1D array corresponding to the name of the label number in the mask

top_num

NULL or a numeric value that used for 1D p-values. If specified, the output will show the top num significant regions. The default is NULL.

p_threshold

NULL or a numeric value that used for 3D p-values 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 3D p-values 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.

multi_pranges

an option under 'scale_p' method to decide whether there are at most 9 colors in the legend for the ranges of 3D p-values, or at most 4 colors. The default is TRUE, choosing the larger number of colors for the plot.

color_pal

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

rank

the method that how the trace is ranked. The default is NULL. There are 2 options: 'value' and a vector. 'value' is to draw the 1D p-values by the values from smallest to largest. a vector is to specific the rank of the regions in 3D p-values plot.

title

the title of the plot. The default is NULL.

Author

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

Details

The function fmri_3dvisual_region is used to visualize the 3D plot of the brain with activated parts region by region. When providing a 1D/3D p-values data, a 3D interactive plot with surface of the brain shell will be generated with either scatter points representing different stimulated levels or large color pieces representing different regions of the brain. When providing a list of two 3D array of p-values, two 3D interactive brains with different scatter points corresponding to the two input 3D p-values will be given.

Examples

# sample label vector provided in the package
label_index = mask_dict$index
label_name = as.character(mask_dict$name)
label_mask = mask_label
# \donttest{
fmri_3dvisual_region(phase1_pval, label_mask, label_index,
                     label_name, title = "phase1 p-values")
fmri_3dvisual_region(phase1_pval, label_mask, label_index,
                     label_name, 5, title = "phase1 top five p-values", rank = "value")

# for 3D visualization, user needs to include empty region in the label
label_index = c(0, label_index)
label_name = c("empty", label_name)
fmri_3dvisual_region(phase2_pval, label_mask, label_index,
                     label_name, title = "phase2 p-values", rank = c(1:length(label_name)))
fmri_3dvisual_region(list(phase2_pval,phase3_pval), label_mask, label_index,
                     label_name, title = "phase2&3 p-values")
# }