Learning engages transient and sustained cellular mechanisms in the human brain

Repository Overview This repository contains all datasets and scripts associated with the manuscript: “Learning engages transient and sustained cellular mechanisms in the human brain” · diff_data_sub-xx Each directory contains multishell diffusion MRI data (NIfTI format) for an individual subject across sessions. Three sessions were acquired: o ses-01: Baseline o ses-02: 30 minutes after learning o ses-03: 24 hours after learning These images were preprocessed using the following pipeline (starting from Connectome scanner output): o Data denoising (MRtrix) o Gibbs ringing correction (MRtrix) o Gradient nonlinearity correction o Susceptibility distortion correction using topup (FSL) o Eddy current and motion correction using eddy (FSL) o Brain mask generation after eddy correction · Data_and_Scripts_Fig_2A_Behavior This directory contains: o Behavioral data from the motor sequence learning task o Performance during ses-01 reflects learning o Performance during ses-02 reflects retention (~24 hours after learning) o Scripts for preprocessing and analysis of MRI and behavioral data. Running these scripts reproduces the results shown in Figure 2A. · Data_and_Scripts_Fig_2B_fMRI This folder contains: o fMRI data for each subject (after gradient nonlinearity correction from Connectome output) o Onset files for each subject indicating task (sequence execution) and rest periods o Statistical results corresponding to Figure 2B (Task > Rest and Rest > Task contrasts) o fMRI signal extracted from DTI-defined ROIs (Supporting Information) o Scripts used for the corresponding preprocessing and analyses using SPM. Note: Subject 30 was excluded from functional analyses due to a technical inconvenience during acquisition affecting most of the dataset. · Data_and_Scripts_Figs_2C_3A_3B_4_Difussion This directory contains: o Final preprocessed SANDI and DTI maps, both in native space and normalized to MNI space o Scripts used for final preprocessing, normalization, and analysis of diffusion MRI data Reproducibility notes: o Running the preprocessing scripts on the diff data in diff_data_sub-xx will reproduce the final preprocessed diffusion images. o Running the statistical analysis (SwE v2.0.0) using the design matrix provided here, together with the ROI extraction scripts, will reproduce the results shown in Figures 2C, 3A, and 3B. Additional contents: o Regions of interest (ROIs) corresponding to clusters shown in Figures 2c, 3a, and 3b o CSV files containing the data used for plotting o Gray matter mask used for diffusion MRI analyses Note: Subject 15 was excluded from diffusion analyses due to a missing session (ses-03). · Data_and_Scripts_Figs_2B_2C_3A_3B_4_T1w_anat This directory contains: o T1-weighted anatomical images (after gradient nonlinearity correction) o Hippocampal subfield segmentations derived from T1 images (FreeSurfer) o Scripts to: § Process hippocampal subfields after FreeSurfer § Register T1 images to diffusion space (native space) § Extract diffusion metrics within hippocampal subfields (Figure 4) · Figures_svg Editable source files for Figures 1-4