nii2png 0.3.0
A lightweight neuroimaging .nii to .png converter
License: MIT

# 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!

1. Input 4D fMRI or 3D MRI NIfTI file (i.e. brain.nii)
2. Rotate orientation of your image
3. Automatically creates .png files for every single slice in every volume.
4. Automatically renames your images with their slice and volume name (i.e. brain_t001_z001.png, etc)
5. 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
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/nii2png.m)

Download Stable Release: [Download](https://github.com/alexlaurence/NIfTI-Image-Converter/releases)

# 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.

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 os

pip install nibabel

pip install numpy
```

## Download nii2png for Python

Download Latest Build: [Download](https://raw.githubusercontent.com/alexlaurence/NIfTI-Image-Converter/master/nii2png.py)

Download Stable Release: [Download](https://github.com/alexlaurence/NIfTI-Image-Converter/releases)

## 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 

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

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/
```