NIfTI to MP4 Converter

A simple Python script to convert 3D NIfTI files (.nii or .nii.gz) into MP4 videos for axial, coronal, and sagittal views.

Features

• Converts a single NIfTI file into three separate MP4 videos (axial, coronal, sagittal).
• Corrects for anisotropic voxel sizes to produce videos with the correct aspect ratio.
• Allows customization of video FPS and intensity normalization range.
• Command-line interface for easy use.

Getting Started

Prerequisites

• Python 3.8+
• git

Installation

1. Clone the repository:

   git clone https://github.com/RivMt/nifti2mp4.git
   cd nifti2mp4

2. Create and activate a virtual environment:

   # Create the environment
   python -m venv venv

   # Activate the environment
   # On Linux/macOS:
   source venv/bin/activate
   
   # On Windows (Command Prompt):
   venv\Scripts\activate.bat
   
   # On Windows (PowerShell):
   .\venv\Scripts\Activate.ps1

3. Install the required packages: A requirements.txt file is provided for managing dependencies.

   pip install -r requirements.txt

Usage

Run the script from your terminal with the virtual environment activated.

python main.py <path/to/input.nii.gz> <path/to/output_prefix>

Arguments:

• input_file: Path to the input NIfTI file (.nii or .nii.gz).
• output_prefix: The prefix for the output MP4 files. This can include a directory path.

Example:

python main.py data/brain.nii.gz results/my_scan

This command will generate three files in the results/ directory:

• results/my_scan-axial.mp4
• results/my_scan-coronal.mp4
• results/my_scan-sagittal.mp4

Note: The script will automatically create the output directory (e.g., results/) if it does not exist.

Command-line Options

You can customize the output with the following options:

• --fps <int>: Sets the frames per second for the output videos. (Default: 30)
• --q_min <float>: Sets the lower percentile for intensity normalization. Values below this will be clipped. (Default: 0.01)
• --q_max <float>: Sets the upper percentile for intensity normalization. Values above this will be clipped. (Default: 0.99)

Example with options:

python main.py data/brain.nii.gz results/my_scan --fps 15 --q_max 0.98

Contributing

Contributions are welcome! If you find a bug or have a suggestion for a new feature, please feel free to open an issue or submit a pull request.