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DCEPrep AUTOMATED PREPROCESSING FOR DCE-MRI STUDIES

Where this fits

DCEPrep automates steps 2 through 6. The full DCEasy pipeline:

1 · Convert DICOM → BIDS dce2bids 2 · Preprocess motion · bias DCEPrep 3 · AIF input function AutoAIF / AIFArtist 4 · T1 map VFA / IR parametric_scripts 5 · PK fit Ktrans · ve · vp ROCKETSHIP + Gpufit 6 · Analyze compare · QC ROCKETSHIP

Explore the DCEasy family →

A preprocessing and analysis pipeline for Dynamic Contrast-Enhanced (DCE) MRI data.

DCEPrep handles the full workflow for measuring permeability (Ktrans) from DCE-MRI acquisitions — from raw DICOM to publication-ready QC reports.

Overview of DCEPrep processing steps

What Does DCEPrep Do?

DCEPrep takes BIDS-organized MRI data and runs a two-phase pipeline:

Phase 1 — Preprocessing (preprocess_all.sh) Prepares raw DCE and VFA images for kinetic modeling. Steps include brain extraction, image registration, bias field correction, z-axis normalization, T1 mapping, and arterial input function (AIF) selection.

Phase 2 — Analysis (DCE_all.sh) Runs pharmacokinetic modeling via ROCKETSHIP to produce Ktrans permeability maps, then generates per-case and population-level HTML/PDF QC reports.

Key Features

  • Fully scriptable — driven by two shell scripts with straightforward CLI flags
  • BIDS-native — expects and produces BIDS-compliant data structures
  • Docker-first — a single container bundles FSL, ANTs, FreeSurfer, MATLAB, and ROCKETSHIP
  • Automated AIF — optional neural-network-based arterial input function detection
  • Variance Reduction — z-axis normalization and bias correction designed to reduce scanner variability
  • Automated QC — per-case and population HTML reports with outlier detection
  • GPU acceleration — Several steps utilize optional CUDA-based acceleration for faster processing

The DCEasy family

DCEPrep is one of several DCEasy tools for DCE-MRI processing, including ROCKETSHIP, AutoAIF, and dce2bids. See dceasy.org for an overview of the full family.

See ROCKETSHIP Integration for details on the MATLAB dependency.

Citation

If you use DCEPrep in your research, please cite:

Barnes S, et al. Automated DCE-MRI processing with DCEPrep for Blood-Brain Barrier permeability in a multi-site aging study. Pending. 2026.