# VisMRI There are three functions in the functions subfolder. - **nifti2df**: after having read a nii.gz file with oro.nifti's readNIFTI function, use this function to transform the 3D matrix into a 2D long data.frame for ggplot - **plotNifti**: function to plot the file created by the above function. ```{r echo=F} library(tidyverse); library(oro.nifti); library(plotly); library(shiny) rm(list=ls()) sapply(list.files("functions",pattern=".R", full.names = T), source) #Read in background image and convert BG = readNIfTI("data/Fix_94_FL12DW_291115_NoDiff/bg_image.nii.gz") %>% nifti2df() #Read in overlay (stats) Cope3 = readNIfTI("data/Fix_94_FL12DW_291115_NoDiff/cope3.feat/stats/zstat5.nii.gz") %>% nifti2df() %>% rename(Cope3=Val) # Add overlay to the df for plotting (will only work with one overlay) IMG = left_join(BG, Cope3, by = c("X", "Y", "Z")) # Try some plotting! plotNifti(BG, view="axial") plotNifti(Cope3, view="sagittal") plotNifti(Dat=IMG, view="sagittal", threshMin=2) plotNifti(Dat=IMG, view="axial", slice=30,threshMin=2.5) ```