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ROCKETSHIP Papers

If you use ROCKETSHIP in your project please reference

Ng et al. ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies. BMC Med Img 2015

in any papers. This reference also has detailed information about the various DCE models used in this project. If you are pursing BBB human applications please consider these papers for parameter suggestions

Barnes et al. Optimal acquisition and modeling parameters for accurate assessment of low Ktrans blood-brain barrier permeability using dynamic contrast-enhanced MRI. MRM 2015

Montagne et al. Blood-brain barrier breakdown in the aging human hippocampus. Neuron 2015

or this for mouse applications

Montagne et al. Pericyte degeneration causes white matter dysfunction in the mouse central nervous system. Nature Medicine 2018

Other Publications using ROCKETSHIP for a more complete list see google scholar

• Sta Maria et al. Low Dose Focused Ultrasound Induces Enhanced Tumor Accumulation of Natural Killer Cells. PLOS One 2015
• Montagne et al. APOE4 leads to blood–brain barrier dysfunction predicting cognitive decline. Nature 2020
• Backhaus et al. Toward precise arterial input functions derived from DCE‐MRI through a novel extracorporeal circulation approach in mice. MRM 2020
• Bagley et al. Clinical Utility of Plasma Cell-Free DNA in Adult Patients with Newly Diagnosed Glioblastoma: A Pilot Prospective Study. Clinical Cancer Research 2020
• Ng et al. Clinical Implementation of a Free-Breathing, Motion-Robust Dynamic Contrast-Enhanced MRI Protocol to Evaluate Pleural Tumors. American Journal of Roentgenology 2020
• Pacia et al. Feasibility and safety of focused ultrasound-enabled liquid biopsy in the brain of a porcine model. Scientific Reports 2020
• Boehm-Sturm et al. Low-Molecular-Weight Iron Chelates May Be an Alternative to Gadolinium-based Contrast Agents for T1-weighted Contrast-enhanced MR Imaging. Radiology 2017

ROCKETSHIP Requirements:

• Matlab Version
  • Verified Working: Matlab 2014a to 2020a
  • Will Not Work: Matlab 2011
• Toolboxes:
  • Curve fitting
  • Parallel
  • Statistics
  • Image processing
  • Optimization (currently required for some functions, working to remove this requirement)
• Computer:
  • Some of the processing is very CPU intensive, a modern multi-core (≥4) processor, while not required, helps keep the processing time reasonable (heavily dependent on image matrix size).
    • (Optional) An NVIDIA GPU can be used to significantly speed up the processing using the gpufit library.

File formats

ROCKETSHIP prefers all images to be input in the NIFTI format. DCE fitting does have some limited support for directly processing DICOM images, but it is recommended to convert from DICOM to NIFTI first, then use the NIFTI images for all processing. Additionally the parametric fitting (T1, T2, ADC) requires NIFTI files. To convert from DICOM to NIFTI we recommend using the dcm2nii tool that comes with MRIcron, it is available for Windows, Linux, and Mac and is easy to use (although any converter can be used). For dcm2nii select the FSL 4D NIFTI format. Compressed NIFTI images (.nii.gz) can be read by ROCKETSHIP, but not written.

Quick Start

1. Clone ROCKETSHIP git clone --recursive https://github.com/petmri/ROCKETSHIP.git
2. Add ROCKETSHIP folder to Matlab path
3. Calculate T1 maps with script run_parametric.m
4. Check T1 maps with script run_analysis.m
5. Calculate DCE maps with script run_dce.m

Walkthroughs

• DCE help
• DSC help
• Parametric (T1, T2, ADC fitting) help

Additional Help

This remains a work in progress. If you need help and can't find it here please contact Sam Barnes [email protected].