XNAT Pipelines Overview

We offer pipelines organized into three main categories: Data Conversion, Quality Control, and Preprocessing

XNAT pipeline Structure

Data Conversion Pipelines

dcm2niix - Converts DICOM files to NIfTI format - Preserves acquisition metadata - Industry standard conversion tool - See: dcm2niix

dcm2bids - Converts DICOM files to BIDS format - Includes BIDS validation and quality checks - Supports custom configuration files - See: dcm2bids

dcm2hcp (Under Development) - Converts DICOM files to HCP format - Optimized for HCP pipeline - See: dcm2hcp (Under Development)

Quality Control Pipelines

mriqc - Comprehensive quality control for structural and functional MRI data - Automated quality metrics and visual reports - Group-level quality analysis and outlier detection - See: MRIQC

ari-validator (Project-Specific) - Validates BIDS datasets for ARI project - Checks file structure, metadata, and parameters - Provides detailed validation reports - See: ari-validator

Preprocessing Pipelines

fmriprep - Robust fMRI preprocessing pipeline - Runs on Jubail HPC cluster - Produces analysis-ready derivatives - See: fMRIPrep

tractoflow - Processes diffusion MRI data - See: TractoFlow

HCP Pipeline (Under Development) - Human Connectome Project-style processing - See: HCP (Under Development)

Next Steps