BIG-S2LabComputations

This repository contains the projects developed within the BIG-S2 Lab at UNC Gillings:

1. ADRD_KG/: A knowledge base website project for Alzheimer's Disease-related datasets and studies. This internal database supports the lab's effort to consolidate and query open-source data on ADRD, aiming to streamline research and data access across projects.

2. ANTs_pipeline/: A collection of shell scripts to simplify the usage of the Advanced Normalization Tools (ANTs) for MRI image preprocessing. These scripts standardize the pipeline execution for structural neuroimaging tasks.

3. TBSS_pipeline/: A collection of shell scripts written to coordinate the TBSS pipeline process.

Structure

.
├── ADRD_KG/ # ADRD knowledge-graph + data wrapping utilities
├── ANTs_pipeline/ # Shell helpers around ANTs for structural MRI
├── TBSS_pipeline/ # Shell helpers to coordinate FSL TBSS
├── YODA_Project/ # Data org + processing templates for YODA datasets
├── LICENSE
└── README.md

ADRD_KG

This project utilized the help of LLM models and the Selenium package to wrap open-source datasets.

ANTs_pipeline

This directory contains only the helper shell scripts used to facilitate the lab ANTs pipeline.

TBSS_pipeline

This directory contains only the helper shell scripts used to facilitate the lab TBSS pipeline.

YODA

This directory contains only the scripts used to facilitate lab research on the YODA project.

Prerequisites

• General: git, Python ≥ 3.10, conda or venv.
• ANTs pipeline: ANTs installed and on PATH; SLURM if submitting to HPC.
• TBSS pipeline: FSL installed and configured; SLURM if using the cluster.
• ADRD_KG: Python + common data/automation libs (see requirements.txt or notebooks inside).
• YODA_Project: Python; access to YODA data (per project policy).

License

This repository is licensed under the MIT License.