Code for the high risk autism phenotype paper
This repository implements a fully reproducible pipeline for the autism signature project. It uses invoke
tasks and a Docker container for consistent, cross-platform execution.
The entire workflow—data fetching, processing, and figure generation—can be reproduced in a few commands.
Much of the code in this repo originated from ASD High Risk Endophenotype Code Supplement and was written by Sebastian Urchs and Hien Nguyen.
All data to reproduce the analysis can be downloaded from
- The study uses data from ABIDE 1 and 2 datasets. Participants were matched using propensity score matching as part of another project, matching scripts can be found here ASD Subtype Code Supplement.
- Resting state functional connectivity data was preprocessed using NIAK, described in the paper. This study uses the seed maps.
- Using the following scripts the full analysis can be reproduced. Alternatively, to skip the data analysis part and recreate the figures, download only the results and atlas data from Zenodo.
🚀 Quick Start
1⃣ Install invoke
First, install invoke
:
pip install invoke
You must also have either Docker or Apptainer installed to use container-based execution.
4⃣ Clean Everything
To remove all generated data:
invoke clean-all
📁 Folder Structure
Folder | Description |
---|---|
source_data/ |
Raw data: Atlases & fMRI data. |
output_data/ |
All generated outputs: Discovery results, figures, etc. |
code/figures/ |
Jupyter notebooks used to generate all figures. |
output_data/Figures/ |
Output folders for each figure notebook. |
tasks.py / tasks_utils.py |
The heart of the pipeline: all invoke tasks live here. |
Building the environment
Installing dependencies
To set up everything, ensure functional Python and R environments and run:
invoke setup-all
This:
- sets up Python & R environments (if running locally);
- prepares the folder structure.
Note: This task assumes an Ubuntu-like OS. You still need to install R, Python, etc. See the Dockerfile for complete setup info.
Note 2:
You can skip this if using the Docker container and running docker-run
directly.
Create a Docker image
To build a Docker image:
invoke docker-build
To generate a compressed archive:
invoke docker-archive
Create an Apptainer image
After building the Docker image, run:
invoke apptainer-archive
This builds the .sif
image from the Docker daemon.
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Created: 11th Apr 2025 at 22:49
Last updated: 11th Jun 2025 at 10:53

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