NIfTI Image Converter (nii2png) for Python and Matlab

Rejoice OpenCV users, a lightweight neuroimaging .nii to .png converter that actually works.

Now supports both Python3 and Matlab 2017b!

Environment

• Python 3.7 (or Matlab 2017b)

Matlab Usage

1. Add your script to your path. And run it simply by typing this and hitting enter:

   nii2png
   

2. Select your working directory.
3. Select your NIfTI image.
4. Rotate your image if you wish:

   >> Would you like to rotate the orientation? (y/n)
   >> y
   >> OK. By 90° 180° or 270°? 
   >> 90
   

5. Let it run.
6. Your png files are now in the png folder of your working directory.

Download nii2png for Matlab 2017b

Download Latest Build: Download

Download Stable Release: Download

Python Setup

For those without Python, Pip or the modules, simply open Terminal and type in the following commands and hit enter.

1. Install Homebrew

   /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
   

2. Install Python 3

   brew install python3
   

3. Install pip

   sudo easy_install pip
   

4. Install plugins

pip install scipy

pip install shutil

pip install nibabel

pip install numpy

pip install imageio

Download nii2png for Python

You can download the latest version of nii2png through pip.

pip install nii2png

Or alternatively, download the binary files here.

Download Latest Build: Download

Download Stable Release: Download

Permissions

If you didn’t install nii2png through pip, you may need to grant nii2png.py permission to execute. On unix systems, Python scripts can be made executable using the following process:

$ chmod +x nii2png.py

Optional: You can also move nii2png.py into your bin directory, and it will be runnable from anywhere.

Python Usage

1. Let’s run the file and start converting images! Please ensure that your output folder ends with a slash to avoid errors.

$ python3 nii2png.py -i <inputfile> -o <outputfolder>

or

$ python3 nii2png.py --input <inputfile> --ouput <outputfolder>

Tip: You can drag and drop the file/folder into the terminal window instead of typing the path

1. Rotate the images if you wish

$ Would you like to rotate the orientation? (y/n) y
$ OK. By 90° 180° or 270°? 90

Example

with change directory command

$ cd ~/images/
$ python3 nii2png.py -i brain.nii -o png/

with full paths

$ python3 /users/ernie/images/nii2png.py -i /users/ernie/images/brain.nii -o /users/ernie/images/png/

with long options

$ python3 /users/ernie/images/nii2png.py --input /users/ernie/images/brain.nii --output /users/ernie/images/png/