SEPIA - SuscEptibility mapping PIpeline tool for phAse images

Abstract

Quantitative susceptibility mapping (QSM) is a physics-driven computational technique that has a high sensitivity in quantifying iron deposition based on MRI phase images. Furthermore, it has a unique ability to distinguish paramagnetic and diamagnetic contributions such as haemorrhage and calcification based on image contrast. These properties have contributed to a growing interest to use QSM not only in research but also in clinical applications. However, it is challenging to obtain high quality susceptibility map because of its ill-posed nature, especially for researchers who have less experience with QSM and the optimisation of its pipeline. In this paper, we present an open-source processing pipeline tool called SuscEptibility mapping PIpeline tool for phAse images (SEPIA) dedicated to the post-processing of MRI phase images and QSM. SEPIA connects various QSM toolboxes freely available in the field to offer greater flexibility in QSM processing. It also provides an interactive graphical user interface to construct and execute a QSM processing pipeline, simplifying the workflow in QSM research. The extendable design of SEPIA also allows developers to deploy their methods in the framework, providing a platform for developers and researchers to share and utilise the state-of-the-art methods in QSM.

QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures

“…The protocol used was that of the QSM challenge (TR = 50 ms; TE 1/2/3/4 = 4/12/20/28 ms; α = 15 23 ). The QSM reconstructions using truncated k‐space division, 66 closed form L2, 67 fast algorithm for nonlinear susceptibility inversion, FANSI 68 and iLSQR 69 as implemented in the SEPIA toolbox, 70 were performed with varying regularization parameters. The reconstructions were evaluated using the reconstructions metrics created for the challenge (Table 2).…”

Open‐source magnetic resonance imaging: Improving access, science, and education through global collaboration

“…In addition to these specific software solutions to drive the console hardware, more general software tools for scanner control, acquisitions, and postprocessing, such as Scanhub, 84,236 are being developed. Scanhub is a cloud-based generic and modular solution enabling integration of many of the aforementioned software packages (e.g., image reconstruction or postprocessing) to be used with actual MR scanner hardware such as the OSI 2 ONE system.…”

QSMxT: Robust Masking and Artefact Reduction for Quantitative Susceptibility Mapping

“…A fully automated solution requires the configuration of a wide range of software tools, making it challenging to setup. However, recent developments in the field, such as the SEPIA toolbox [29], attempt to provide extensible frameworks for QSM processing, enabling a wide range of algorithms to be supported by a single and easy-to-use tool, though several steps are unaccounted for, manual intervention is required, and processing does not scale well for large datasets.…”