A lightweight neuroimaging .nii to .png converter
Project description
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!
- Input 4D fMRI or 3D MRI NIfTI file (i.e. brain.nii)
- Rotate orientation of your image
- Automatically creates .png files for every single slice in every volume.
- Automatically renames your images with their slice and volume name (i.e. brain_t001_z001.png, etc)
- Automatically moves all your images into a chosen folder within your working directory.
Unlike other tools out there, this just works.
Environment
- Python 3.7 (or Matlab 2017b)
Matlab Usage
- Add your script to your path. And run it simply by typing this and hitting enter:
nii2png
- Select your working directory.
- Select your NIfTI image.
- Rotate your image if you wish:
>> Would you like to rotate the orientation? (y/n)
>> y
>> OK. By 90° 180° or 270°?
>> 90
- Let it run.
- 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
Modules
- scipy
- shutil
- os
- nibabel
- numpy
Basic Setup
For those without Python, Pip or the modules, simply open Terminal and type in the following commands and hit enter.
- Install Homebrew
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
- Install Python 3
brew install python3
- Install pip
sudo easy_install pip
- Install plugins
pip install scipy
pip install shutil
pip install os
pip install nibabel
pip install numpy
Download nii2png for Python
Download Latest Build: Download
Download Stable Release: Download
Permissions
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
- 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
- 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/
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