A guide to advanced MRI processing for clinical glioma research

BackgroundTo date, multiple advanced magnetic resonance imaging (MRI) methods beyond conventional qualitative structural imaging for the diagnosis, prognosis, and treatment follow-up of glioma have demonstrated their utility for clinical studies. However, these methods often rely on complex off-scanner processing to yield the most information and to extract quantitative biomarkers, limiting their practical use for studies, as well as their clinical translation.While community-driven software solutions exist for these advanced MRI methods, many aspiring clinical researchers face challenges in acquiring the necessary knowledge to effectively apply these tools. This guide, an initiative of the Glioma MR imaging 2.0 network (GliMR), aims to provide an overview of existing solutions, communities, and repositories with the ultimate goal of enabling standardization, open science, and reproducible quantitative imaging studies of gliomas. Yet, most of the reviewed tools and approaches to image data analyses may also be used in the context of studies on diseases other than glioma.ContentThis guide summarizes the state-of-the-art processing software solutions and the repositories/communities for the following advanced MRI methods: DSC; DCE; ASL; diffusion MRI; relaxometry; MRF; MRS; CEST; SWI; QSM; MRE; and task-based and resting-state fMRI. For each of those, after a short introduction about the method and output parameters, the required and recommended image processing steps and quality control measures are described, and we point to further literature for more details. In addition, an overview of openly available software tools that provide these functionalities for MRI processing and exemplify workflows is given. Wherever possible, the readers are guided toward existing inventories, repositories, and communities, which offer not only a collection of these tools, but also more in-depth guidance. Each part concludes with an appraisal of the estimated required expertise and future development needs.ConclusionThis guide provides an extensive overview of the currently available processing tools that can help aspiring clinical researchers to obtain high-quality reproducible imaging data from advanced MRI scans of gliomas. While GliMR n is focused on glioma research, this guide will also be helpful for other clinical neuroimaging topics as general processing steps may not be specific to glioma only.