LifespanTrajectoryChimpanzees

Analysis code for "Lifespan trajectory of chimpanzee brains characterized by magnetic resonance imaging histology"

Overview

This repository contains analysis scripts for processing and comparing human and chimpanzee brain MRI data, with a focus on lifespan trajectories and cortical measurements.

Repository Structure

In Vivo Human Data Analysis

• human_maskingSPM_Script.m - MPM (Magnetization Parameter Mapping) generation
• human_PreProcScriptMPM_subjList_hMRI.csh - Segmentation preparation
• freesurfer_processing_steps_human.txt - Segmentation steps
• human_post_freesurfer_pipeline_human_reg_dat - Post-segmentation processing

Main Analysis Scripts

• chimp_to_human_harmonisation.m - Harmonizes cortical measurements between chimpanzee and human brain data
• group_freesurfer_analysis_chimps - FreeSurfer group analysis for chimpanzee data
• group_freesurfer_analysis_humans - FreeSurfer group analysis for human data
• exclude_projection_outliers_for_group_freesurfer - Outlier detection and correction in cortical surface projections
• group_freesurfer_analysis_humans_vs_chimps - Vertex-wise comparisons between human and converted chimp data
• group_freesurfer_result_plots_including_humans.m - Visualization of harmonized cortical measurements
• microstructural_application_pipeline_attempt - ROI analysis, intracortical profiles, and developmental modeling

Functions

The functions directory contains various utility functions used by the main analysis scripts.

Related Resources

Postmortem chimpanzee data analysis code is available in a separate repository: postmortembrain-mpm

License

This work is licensed under a Creative Commons Attribution 4.0 International License.

This means you are free to:

• Share — copy and redistribute the material in any medium or format
• Adapt — remix, transform, and build upon the material for any purpose, even commercially

Under the following terms:

• Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made.

Citation

to come soon

Contact

Ilona Lipp, [email protected]