Hippocampus_cortex_gradient_youth

Code and data for the manuscript entitled "Hippocampus reorganizes its function and geometry along a dual long-axis for cognitive maturation in youth" by Zeng et al.

File descriptions

The code files are located within the Code/ directory,

1. compute_gradient_avg_all.m: This script computes group-averaged hippocampal-cortical connectome gradients, visualizes these gradients on mid-thickness surfaces, and tests the relationships between hippocampal gradients and AP/PD coordinates.
2. hippgrad_ctx_projection.m: In this script, the cortical projection of hippocampal gradients is computed. It also visualizes the group-averaged projection map and tests the relationships between cortical projection maps and cortical functional hierarchy (FH).
3. hippvol_eigenmode_calculation.sh: This script computes the Laplacian eigenmodes for each individual hippocampus.
4. compute_gradient_geometry_coupling.m This script computes the coupling between individual hippocampal gradients and their geometric eigenmodes. It visualizes the group-averaged geometric eigenmodes and tests the relationships between group-averaged geometric eigenmodes and group-level functional gradients.
5. G_feat_age_gam.R: This script fits the developmental trajectories of explained variance and distribution characteristics corresponding to hippocampal gradients.
6. Mye_bins_age_gam_HCD.R: This script fits the developmental trajectories of mean T1w/T2w intensity within each of the uniform partitioned bins along the group-averaged myelin content axis.
7. G_bins_age_gam_HCD.R: This script fits the developmental trajectories of mean gradient values within each of the uniform partitioned bins along the group-averaged myelin content axis.
8. G_CTX_FH_age_gam.R: This script investigates the developmental pattern of the association between individual gradient projections and the adult cortical FH map.
9. G_CTX_proj_LR_age_gam.R: This script characterizes the maturational changes in hippocampal gradient projections in individual cortical regions. Please note that running this analysis may take approximately 6 minutes.
10. EigMod_G_age_gam.R: This script models the age-related trajectory of the coupling between hippocampal geometric modes and their corresponding gradients.
11. Brain_behavior_association.m: This script tests the relationship between Executive Function performance and the geometric-functional coupling of lLG.
12. Brain_behavior_association_agegrp.m: This script tests the relationship between Executive Function performance and the geometric-functional coupling of qLG within specific age groups.

Additionally, intermediate processing results produced by the above scripts are included in Results/. These include group-averaged hippocampal-cortical connectivity and corresponding gradients, group-averaged cortical projections of hippocampal gradients, and group-averaged hippocampal geometric eigenmodes.

Installation

Download the repository, and you will find all the MATLAB dependencies in Dependencies/Matlab/. All MATLAB codes are ready to use. The R packages can be installed using the install.packages() method.

For the Python codes, set up the environment based on the *_package_list.txt in Dependencies/Python/.

Downloading data

We provide example data for one subject in the Data/ directory, which includes hippocampal fMRI and cortical fMRI data, output files from Hippunfold, and files related to hippocampal geometric eigenmodes. You can download this data from _.

You can download the transcription data from the Allen Human Brain Atlas site and get the renormalized sample coordinates in MNI space at here.

Original data

The original and preprocessed HCP-D data, after meeting eligibility requirements, can be accessed here.

Dependencies

Some of the dependency packages, especially those with modifications, have been stored in the Dependencies/ folder to ensure version compatibility.

1. Hippocampal gradient computation and visualization:

• cifti-matlab(v2.1.0)

• gifti

• BrainSpace tool(v0.1.10) with modifications in plotter.m used by plot_hemispheres.m for enhanced brain visualization

• gramm

• SurfStat with modifications to include additional useful functions

2. Hippocampal geometric eigenmodes computation:

• Partially adapted from BrainEigenmodes by Pang et al.

• Dependencies: FSL, FreeSurfer, Connectome Workbench, and Gmsh software

• Python environment details in Dependencies/Python/BrainEigMod_package_list.txt.

3. Transcriptomic association and gene enrichment analysis of hippocampal gradients:

• Partially adapted from Hippocampus_AP_Axis by Vogel et al.

• Python environment details in Dependencies/Python/Hipp_Gene_package_list.txt.

• Metascape web tool

• Developmental-specific expression analysis (SEA) tool

4. Analysis of developmental effects:

• R packages: mgcv(v1.8-42) and gratia(v0.8.1)

Compatibility

The code has been tested on Python 3.8, MATLAB R2018a, and R 4.2.3.

Citation

If you use our code in your research, please cite us as follows:

[PREPRINT] D. Zeng, Q. Li, D. Li, ..., Y. He, X. Zuo, S. Li, Dual long-axis reorganization of hippocampus in youth, bioRxiv (2023) (DOI: 10.1101/2023.11.03.565423)

Further details

Please contact [email protected] if you need any further details.