Make a GIF animation from a set of brain MRI DICOM images

T1_brain_MRI_make_gif.R

# Copyright (c) 2018 Alexej Gossmann
# MIT License https://choosealicense.com/licenses/mit/

library(oro.dicom)
library(oro.nifti)
library(fslr)
library(R.matlab)
library(tidyverse)
library(gganimate)
library(doParallel)
registerDoParallel(cores = 3)

t1_data_dir <- "/path/to/DICOMs/"

all_slices <- readDICOM(t1_data_dir)
t1_brain_nii <- dicom2nifti(all_slices)
n_slices <- length(all_slices[["img"]])

slice_to_df <- function(brain_nii, slice_num) {
  tmp_mat <- brain_nii@.Data[ , , slice_num]
  colnames(tmp_mat) <- 1:ncol(tmp_mat)
  tmp_df <- as_data_frame(tmp_mat) %>%
    mutate(row_id = 1:nrow(tmp_mat)) %>%
    gather(col_id, value, -row_id) %>%
    mutate(col_id = as.integer(col_id)) %>%
    mutate(slice = slice_num)
  return(tmp_df)
}

t1_brain_df <- foreach(i = 1:n_slices, .combine = bind_rows) %dopar% {
  slice_to_df(t1_brain_nii, i)
}

p <- ggplot(t1_brain_df) +
  geom_tile(aes(x = row_id, y = col_id, fill = factor(value), frame = slice)) +
  scale_fill_grey() +
  theme_void() +
  theme(plot.title = element_text(color = "#CCCCCC"), legend.position = "none",
        plot.background = element_rect(fill = "#333333", color = NA)) +
  coord_fixed(ratio = pixdim(t1_brain_nii)[2]) +
  ggtitle("Slice")

# width and height set by hand to avoid white borders around the plot
w <- 374
h <- 485
gganimate(p, "T1.gif", interval = 0.1, title_frame = TRUE,
          ani.width = w, ani.height = h)