Healthy Human Brain Development Analysis

This repository contains a comprehensive Jupyter Notebook that explores healthy human brain development using 3D MRI scans from the IXI dataset. The analysis focuses on understanding brain structure evolution by processing and analyzing high-resolution MRI data through a systematic pipeline. Overview

The project leverages advanced neuroimaging techniques to:

Extract the brain from raw MRI scans.
Register the scans to a standard space using a well-established atlas.
Create masks for specific brain regions based on the Harvard-Oxford cortical and subcortical atlas.
Estimate regional brain volumes.
Perform a detailed analysis of the healthy brain development across subjects.

Pipeline Details

Brain Extraction:
Isolate the brain from non-brain tissues in the MRI scans to focus the analysis on the regions of interest.

Registration with Atlas (Standard Space):
Align each brain scan to a common coordinate system using the Harvard-Oxford atlas, ensuring consistency across subjects.

Creating Region-Specific Masks:
Generate masks for specific brain regions using the atlas to facilitate targeted volumetric analyses.

Volume Estimation:
Compute the volume of selected brain regions to assess structural differences and developmental trends.

Analysis:
Analyze the extracted and computed data to draw insights into healthy human brain development, including potential growth patterns and structural variations.

Credits

MRI Scans:
The 3D MRI scans utilized in this analysis are provided by the IXI dataset. We extend our gratitude to IXI for making these resources available.

Atlas:
The registration and mask creation were performed using the Harvard-Oxford cortical and subcortical atlas. Thanks to the developers for their invaluable contribution to neuroimaging research.