PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images

Abstract

Diffusion weighted MRI imaging (DWI) is often subject to low signalto-noise ratios (SNRs) and artifacts. Recent work has produced software tools that can correct individual problems, but these tools have not been combined with each other and with quality assurance (QA). A single integrated pipeline is proposed to perform DWI preprocessing with a spectrum of tools and produce an intuitive QA document. Methods: The proposed pipeline, built around the FSL, MRTrix3, and ANTs software packages, performs DWI denoising; inter-scan intensity normalization; susceptibility-, eddy current-, and motion-induced artifact correction; and slice-wise signal drop-out imputation. To perform QA on the raw and preprocessed data and each preprocessing operation, the pipeline documents qualitative visualizations, quantitative plots, gradient verifications, and tensor goodness-of-fit and fractional anisotropy analyses. Results: Raw DWI data were preprocessed and quality checked with the proposed pipeline and demonstrated improved SNRs; physiologic intensity ratios; corrected susceptibility-, eddy current-, and motion-induced artifacts; imputed signal-lost slices; and improved tensor fits. The pipeline identified incorrect gradient configurations and file-type conversion errors and was shown to be effective on externally available datasets.

Integrated Diffusion Image Operator (iDIO): A tool for automated configuration and processing of diffusion MRI data

“…iDIO produces the QC report for each dataset in a single PDF file when preprocessing is completed. Most of the dMRI preprocessing steps have corresponding QC results (Figure 1 with QC labels), which were generated mostly from EddyQuad and PreQual (Bastiani et al, 2019; Cai et al, 2021). The QC report embeds a method summary, and warning messages are given when applicable.…”

“…Here, we present the 'integrated Diffusion Imaging Operators' or iDIO, which aims to be a user-friendly one-click solution for dMRI data processing based upon advanced software tools. The workflow of iDIO encapsulates parts of the functionalities of ANTs (Avants et al, 2009), FSL (Jenkinson et al, 2012), MRtrix3 (Tournier et al, 2019), and Prequal (Cai et al, 2021). iDIO supports dMRI data acquired with different clinical MRI vendors, such as Siemens, GE, Philips, and United Imaging.…”

“…Advanced software packages have provided individual functions to conduct specific or combined data processing, such as ANTs, FSL, PreQual, and MRtrix3 (Avants et al, 2009; Jenkinson et al, 2012; Tournier et al, 2019; Cai et al, 2021). Several processing pipelines have also been proposed to deal with the variations in image acquisition schemes (Smith and Connelly, 2019; Theaud et al, 2020; Cai et al, 2021; Cieslak et al, 2021; Joseph et al, 2021). These tools can improve the comparability or generalizability of the research findings across studies.…”

What’s new and what’s next in diffusion MRI preprocessing

“…Various software packages and pipelines have included this bias field correction as an optional step in the image prepocessing pipeline, e.g. MRtrix ( Tournier et al, 2019 ), FSL ( Jenkinson et al, 2012 ), QSIprep (Cieslak et al, 2020), Tractoflow ( Theaud et al, 2020 ), PreQual ( Cai et al, 2021b ), and DESIGNER ( Ades-Aron et al, 2018 ). However, when applied, the signal scaling will be another source of noise heteroscedasticity in the data (similar to Fig.…”

MASiVar: Multisite, Multiscanner, and Multisubject Acquisitions for Studying Variability in Diffusion Weighted Magnetic Resonance Imaging

“…After acquisition, all scans in MASiVar were preprocessed and quality checked with the PreQual pipeline (23). In brief, all acquisitions per scan were denoised with the Marchenko-Pastur technique (24)(25)(26), intensity normalized, and distortion corrected.…”