Convert DICOM Files to PNG

Important Changes

• 8/26/2018 - Ability to apply auto-contrast to the converted images

Introduction

A simple python module to make it easy to batch convert a binary DICOM file, which is usually an output from an MRI scan to a PNG image.

The MRI scanning facilities typically hand you a CD containing your MRI scans. This CD will typically not contain any image files in traditional formats that can be opened up by your default image viewing program. The CD contains a list of DICOM files, which can only be viewed by the included viewer, which is mostly only supported on a Windows machine.

This module should help you convert all the DICOM based scans to PNG files. This tool can be used as a command line tools as well as a library in your python code

Installation

To have known to work dependencies use beforehand::

pip install -r requirements.txt

mritopng comes with a setup.py script to use with distutils. After unpacking the distribution, cd into the directory and execute the command::

python setup.py install

This will install two things

• The mritopng module will be installed; import mritopng will allow you to use it
• A command line utility called mritopng which can be used from the console

Quick Start

mritopng will install a command line utility that can be used to convert individual DICOM files or folders

Getting Help

$ mritopng --help
usage: mritopng [-h] [-f] [-c] dicom_path png_path

Convert a dicom MRI file to png. To conver a whole folder recursivly, use the
-f option

positional arguments:
  dicom_path           Full path to the mri file
  png_path             Full path to the generated png file

optional arguments:
  -h, --help           show this help message and exit
  -f, --folder         Convert a whole folder instead of a single file
  -c, --auto-contrast  Apply contrast after converting default image

Convert Single File

# Converts the file /DICOM/SCAN1 to a file called output.png,
# while applying auto contrast
$ mritopng --auto-contrast /DICOM/SCAN1 output.png

Note: If file output.png already exists, it will be overwritten

Convert Folder Tree

The utility can also be used to convert a whole folder recursively by using the -f option::

# Takes all the files in /DICOM, converts the files to png and
# puts them in the /PNG folder with the same structure as /DICOM. 
$ mritopng -f /DICOM /PNG

Note:

• Existing top level folder will NOT be over-written e.g. the example above will fail of the folder /PNG already exists
• The tool will try to convert as many files as it can, skipping the ones that it can't

Using it as a Library

It's pretty easy to get up and running with mritopng in your own project

import mritopng

# Convert a single file with auto-contrast
mritopng.convert_file('/home/user/DICOM/SCAN1', '/home/user/output.png', auto_contrast=True)

# Convert a whole folder recursively
mritopng.convert_folder('/home/user/DICOM/', '/home/user/PNG/')