🧠 NeuroImg2PNG: Efficient Neuroimaging Conversion 🖼️

Overview

Welcome to the NeuroImg2PNG repository! This project is designed to streamline the process of converting neuroimaging files, specifically .nii files, into PNG images. Leveraging Google Colab and Google Drive integration, this notebook provides an efficient way to handle large neuroimaging datasets without the hassle of excessive data transfer.

✨ Features

• 🌐 Google Drive Integration: Directly access and save files on Google Drive, reducing the need for data upload/download.
• 🚀 Efficient Decompression: Automatically uncompress .nii.gz files to .nii format within your Google Drive directory.
• 🌀 4D fMRI to PNG Conversion: Converts 4D fMRI scans into PNG images, looping through time points.
• 📸 3D sMRI to PNG Conversion: Converts 3D sMRI scans into PNG images.
• 📊 Optimized for Bandwidth: Minimizes data usage and bandwidth by handling all operations within Google Drive and Google Colab.

🛠️ How It Works

Step 1: Setup

First, the notebook installs the necessary libraries for neuroimaging data processing.

Step 2: Library Imports

Key libraries such as nibabel, numpy, matplotlib, and cv2 are imported to handle neuroimaging data and image processing.

Step 3: Google Drive Mounting

Mount your Google Drive to access and store files directly from your cloud storage. This integration ensures that large files are managed efficiently.

Step 4: Directory Setup

Specify the directories in your Google Drive where your .gz compressed files and output images will be stored.

Step 5: Data Cleansing and Extraction

The notebook scans the specified directory for .nii.gz files, decompresses them to .nii format, and saves them in the same directory. This process ensures that you have uncompressed .nii files ready for conversion without additional data transfer.

Step 6: Conversion to PNG

• 🌀 fMRI Conversion: The notebook loops through the time points of 4D fMRI scans, converting each slice into a PNG image and saving them in the specified output directory.
• 📸 sMRI Conversion: Similarly, 3D sMRI scans are converted to PNG images and saved.

🌟 Why This Approach?

By leveraging the power of Google Colab and Google Drive, this notebook provides a seamless and efficient workflow for handling large neuroimaging datasets. Users benefit from reduced data transfer times, optimized bandwidth usage, and the convenience of cloud-based storage and processing.

💡 Highly Recommended Environment

This notebook is highly recommended to be used on Google Colab due to its seamless integration with Google Drive and the computational resources it provides, making it ideal for handling large neuroimaging datasets.

🚀 Getting Started

1. Clone the Repository: Clone this repository to your local machine or directly open the notebook in Google Colab.
2. Mount Google Drive: Follow the instructions in the notebook to mount your Google Drive.
3. Set Directories: Specify the paths to your .gz files and the desired output directories.
4. Run the Notebook: Execute the cells to decompress, convert, and save your neuroimaging files as PNG images.

🎉 Conclusion

NeuroImg2PNG simplifies the conversion of neuroimaging files, making it accessible and efficient for researchers and practitioners. By integrating cloud-based tools, this project ensures that you can handle large datasets with ease and minimal resource usage.

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Stay in Touch 📬

Thank you for using NeuroImg2PNG! If you have any questions or need any more help, please feel free to reach out.

https://shorturl.at/nQqEd