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YY Preprocessing Documentation

Welcome to the documentation for yyprep - a comprehensive tool for DICOM to BIDS conversion and fMRIPrep preprocessing, developed for Prof. Yaara Yeshurun's Lab.

What is yyprep?

YY Preprocessing (yyprep) is a Python package that streamlines neuroimaging data preprocessing workflows by providing:

  • DICOM to BIDS conversion using HeuDiConv with automatic fieldmap handling
  • fMRIPrep preprocessing through a simplified nipype-compatible interface
  • Unified command-line interface for complete preprocessing pipelines
  • Python API for programmatic workflow control

Quick Start

Installation

pip install yyprep

Basic Usage

# Convert DICOM to BIDS
yyprep dicom2bids participants.csv --bids-dir /path/to/bids --heuristic heuristic.py

# Run fMRIPrep preprocessing
yyprep fmriprep /path/to/bids /path/to/output participant --participant-label 001 002

Documentation Sections

Getting Started

User Guide

Advanced Topics

Development

Examples

Explore complete examples in our examples directory:

  • Complete Jupyter Notebook: tzlil_preprocessing.ipynb - End-to-end preprocessing workflow
  • Python Script: fmriprep_usage.py - fMRIPrep integration examples

Features

✅ DICOM to BIDS Conversion - Automated conversion using HeuDiConv - Custom heuristic support - Automatic fieldmap IntendedFor handling

✅ fMRIPrep Integration - Nipype-compatible interface - Docker-based execution via fmriprep-docker - Comprehensive parameter support

✅ Unified CLI - Single command for complete pipelines - Flexible parameter configuration - Dry-run capabilities

✅ Python API - Programmatic workflow control - Integration with existing pipelines - Jupyter notebook support

Support