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https://github.com/alexlaurence/nifti-image-converter
🖼 A lightweight neuroimaging .nii to .png converter for Matlab and Python users
https://github.com/alexlaurence/nifti-image-converter
convert-images converter matlab medical-imaging neuroimaging nifti opencv png python
Last synced: 6 days ago
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🖼 A lightweight neuroimaging .nii to .png converter for Matlab and Python users
- Host: GitHub
- URL: https://github.com/alexlaurence/nifti-image-converter
- Owner: alexlaurence
- License: mit
- Created: 2019-05-07T18:50:14.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-04-28T08:58:41.000Z (5 months ago)
- Last Synced: 2024-09-24T23:02:09.958Z (9 days ago)
- Topics: convert-images, converter, matlab, medical-imaging, neuroimaging, nifti, opencv, png, python
- Language: Python
- Homepage: https://alexlaurence.github.io/NIfTI-Image-Converter/
- Size: 81.1 KB
- Stars: 117
- Watchers: 2
- Forks: 39
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE
Awesome Lists containing this project
README
# 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](https://raw.githubusercontent.com/alexlaurence/NIfTI-Image-Converter/master/matlab/nii2png.m)
Download Stable Release: [Download](https://github.com/alexlaurence/NIfTI-Image-Converter/releases)
# 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](https://raw.githubusercontent.com/alexlaurence/NIfTI-Image-Converter/master/python/nii2png.py)
Download Stable Release: [Download](https://github.com/alexlaurence/NIfTI-Image-Converter/releases)
## 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 -o
```
or
```
$ python3 nii2png.py --input --ouput
```
Tip: You can drag and drop the file/folder into the terminal window instead of typing the path
2. 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/
```