Takes a *stamp* volume file (such as a single label image of an oil capsule on the left side of the temple) and adds it to each image in the input directory and writes the resulting images to the output directory. The stamp file must match the dimensions of all the image files.

volume_stamper.py

#!/usr/bin/python

# created on 18/5/13 by Nat Noordanus [email protected]

import os, argparse


parser = argparse.ArgumentParser()
parser.add_argument("input_dir")
parser.add_argument("stamp_file")
parser.add_argument("output_dir")
args = parser.parse_args()

input_dir = args.input_dir
stamp_file = args.stamp_file
output_dir = args.output_dir

while input_dir[-1] == "/":
    input_dir = input_dir[0:-1]
while stamp_file[-1] == "/":
    stamp_file = stamp_file[0:-1]
while output_dir[-1] == "/":
    output_dir = output_dir[0:-1]


# to convert nrrd file from seg3d to nifit run `c3d <inputfile.nrrd> -o <outputfile.nii>`

valid_extensions = [".nii", ".nii.gz", ".nrrd"]
input_images = [item for item in os.listdir(input_dir) if any(item.endswith(ext) for ext in valid_extensions)]

for input_file in input_images:
  input_file_path = input_dir+'/'+input_file
	output_file_path = output_dir+'/'+input_file.split('.')[0] + '.nii'
	# use option like -flip x if neccessary
	command = 'c3d ' + stamp_file +' -scale 250 '+ input_file_path + ' -add -o ' + output_file_path 
	os.system(command)