Gideon Temp – Data Harmonization Pipeline

This repository contains a temporary data pipeline for harmonizing behavioral and MRI data into BIDS format.

Purpose

This repository serves as a temporary workspace for developing and testing a data harmonization pipeline.
The goal is to transform raw source data (behavioral and MRI) into a BIDS-compliant dataset.

It is not intended as a production-ready pipeline but as an intermediate development environment.

Overview of the Pipeline

The pipeline:

• Ingests raw behavioral data and MRI data from source directories
• Standardizes file naming and structure
• Maps metadata into BIDS-compatible fields
• Generates BIDS-compliant directory structure
• Prepares datasets for downstream neuroimaging analysis

The output dataset follows the Brain Imaging Data Structure (BIDS) specification: https://bids.neuroimaging.io/

Validation can be performed using the BIDS Validator.

Output

The pipeline produces a BIDS-formatted dataset:

data/raw/
├── sub-01/
│   ├── anat/
│   ├── func/
│   └── beh/
├── dataset_description.json
└── participants.tsv

Status

Work in progress

• Behavioral harmonization complete
• MRI conversion integrated
• Automated BIDS validation