MRINavigator

Magnetic Resonance Imaging Navigator-based corrections

Table of contents

• MRINavigator
• • Table of contents
  • Introduction
  • Installation
  • Testing MRINavigator
  • Updating MRINavigator
  • Navigator-based correction
  • Plotting
  • Acknowledgements
  • Citing this work
• Get started
• • Data requirements
  • Data reshaping
  • The parameters dictionary
  • User examples
  • Disclaimer
• Navigator-based correction pipelines
• API
• Run compact pipeline
• • Coil sensitivity maps
  • Find centerline
  • Utils
  • Navigator correction
  • Adjust data

Introduction

MRINavigator provides multiple navigator-based correction pipelines for Magnetic Resonance (MR) images. These aim at demodulating time-dependent field variations present in multi echo-gradient echo acquisitions. The package was developed with a focus on spinal cord imaging, but it can be used for multiple imaging applications. The corrections are to be applied to the raw data before the image reconstruction. MRIReco.jl can be used to reconstruct the images.

Installation

Start julia and open the package manager REPL mode by entering ]. Then enter

pkg> add MRINavigator

This will install MRINavigator and all its dependencies. If you want to develop MRINavigator itself you can checkout MRINavigator locally as usual by calling

pkg> dev MRINavigator

More information on how to develop a package can be found in the Julia documentation.

Requirements

To use some package functionalities, external softwares are necessary. These include:

• Spinal Cord Toolbox (SCT)
• FSLeyes

Using these toolboxes should improve the correction outcome of the pipelines including a Fourier transform (FFT) step. Use of SCT and FSLEyes is only relevant for spinal cord acquisitions. For additional information read the Get started and Navigator-based correction pipelines sections.

Testing MRINavigator

To make sure that the package is correctly installed, start julia from the command line, type ] to enter the package manager REPL mode. Then enter

pkg> test MRINavigator

Updating MRINavigator

To update MRINavigator to the latest version, start julia from the command line, type ] to enter the package manager REPL mode. Then enter

pkg> update MRINavigator

Navigator-based correction

Multi-echo gradient-echo (GRE) sequences are commonly acquired both in research and clinical practice. However, one of their main limitations is the sensitivity to field instabilities both in space and time. Indeed, for the signal spatial encoding to be effective, a background homogeneous field in time and space is required. Time-varying background fields can lead to phase modulation between k-space lines, and therefore TE-dependent ghosting artefacts. Navigator readouts in the k-space center can be used to measure the intensity of the field fluctuations,enabling correct demodulation of the acquired signal before image reconstruction. The standard navigator-based correction was developed for brain imaging and it is not robust when applied in other areas e.g. the spinal cord. When failing, the correction can even exacerbate the problem. This package provides optimized post-processing pipelines to correct for dynamic field instabilities in GRE sequences. For additional information read the Navigator-based correction pipelines section.

Plotting

MRINavigator does not depend upon a particular plotting package since there are various plotting packages available in Julia. Feel free to use your package of choice.

Acknowledgements

This package uses the reconstruction functions and data structures available in MRIReco.jl. T. Knopp and M. Grosser (2021). MRIReco.jl: An MRI Reconstruction Framework written in Julia. Magnetic Resonance in Medicine. 2021.

Citing this work

If you use MRINavigator in you research please cite the following:

Optimised navigator correction of physiological field fluctuations in multi-echo GRE of the lumbar spinal cord at 3T. L Beghini, G David, M D Liechti, S Büeler, S J Vannesjo. 2023. Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM).