dcm2niix

Note

For step-by-step instructions on running any pipeline, see Running Pipelines on XNAT. To enable pipelines for your project, see Enabling Pipelines for Your Project. For running pipelines across multiple subjects in parallel, see Running Pipelines Across Multiple Subjects.

The dcm2niix pipeline converts DICOM files to NIfTI format for analysis compatibility.

Overview

The dcm2niix pipeline provides: - DICOM to NIfTI conversion using the industry-standard dcm2niix tool - Metadata preservation in JSON sidecar files - Automatic handling of multi-echo and complex data - Quality control and validation checks

Input Requirements

Required: - DICOM files organized in XNAT sessions - Valid XNAT project with appropriate permissions

Supported Data Types: - Structural MRI (T1w, T2w, FLAIR, etc.) - Functional MRI (BOLD, ASL) - Diffusion MRI (DWI, DTI) - Fieldmap data

How to Run

For general instructions on running pipelines, see: Running Pipelines on XNAT

Pipeline-Specific Parameters: - Output format: NIfTI (.nii.gz) - Metadata export: JSON sidecar files - Naming convention: BIDS-compatible names - Quality control: Automatic validation

Output Structure

Generated Files: - *.nii.gz - NIfTI image files - *.json - Metadata sidecar files - conversion_report.txt - Conversion log - validation_summary.html - Quality control report

File Organization: - Files organized by scan type and sequence - Consistent naming across subjects - Metadata preserved in JSON format

Troubleshooting

Common Issues: - Incomplete conversions: Check for corrupted DICOM files - Missing metadata: Verify DICOM header completeness - Orientation issues: Review spatial orientation settings

Quality Control: - Verify image orientation and dimensions - Check metadata completeness - Validate conversion accuracy

Next Steps