Functional gradients dissociate between cortical layers

This repository contains the complete pipeline to reproduce the analyses and figures from the manuscript:

Functional gradients dissociate between cortical layers Degutis, J.K. et al. (2026)

Repository structure

.
├── src/
│   ├── preprocessing/          # fMRI preprocessing pipeline
│   │   ├── fmri-analysis       # submodule for preprocessing from https://github.com/dchaimow/fmri_analysis/tree/main/library
│   ├── restingState/           # main resting-state analysis
│   │   ├── runRestingState_inter.py   # entry point for the main analysis
│   │   └── laminar_rs/         # analysis functions
│   └── robustness/             # robustness / control analyses
├── demo/                       # standalone, minimal demo (see demo/README.md)
├── environment.yml             # conda environment specification
└── requirements.txt            # pip requirements + external-tool provenance

A small, self-contained demo that reproduces the core analysis on a single precomputed matrix lives in demo/ and is documented separately in demo/README.md.

Installation

Create the conda environment (recommended):

conda env create -f environment.yml
conda activate laminar-analysis

Total instalation time may take 30-60 minutes.

Note. The pipeline also relies on external neuroimaging software (FreeSurfer, ANTs, AFNI, LAYNII, SPM12/CAT12, ciftify, Connectome Workbench). Install them separately. Required versions are listed at the bottom of requirements.txt.

Usage

The main resting-state analysis is run from src/restingState/:

This estimates the gradients, computes the inter-areal laminar dissimilarity, and produces the associated surface maps and figures. The analysis functions it calls are organised under src/restingState/laminar_rs/.

Preprocessing scripts are provided in src/preprocessing/, and the robustness / control analyses reported in the manuscript are in src/robustness/.

All analyses were run inside a Singularity/Apptainer container bootstrapped from the Docker image ubuntu:22.04 (Ubuntu 22.04 LTS, Jammy Jellyfish; amd64).

Citation

If you use this code, please cite:

Degutis, J.K. et al. (2026). Functional gradients dissociate between cortical layers.

Contact

For questions, please contact:

📧 j.karolis.degutis (at) gmail.com