PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images. Issue 1 (3rd February 2021)
- Record Type:
- Journal Article
- Title:
- PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images. Issue 1 (3rd February 2021)
- Main Title:
- PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images
- Authors:
- Cai, Leon Y.
Yang, Qi
Hansen, Colin B.
Nath, Vishwesh
Ramadass, Karthik
Johnson, Graham W.
Conrad, Benjamin N.
Boyd, Brian D.
Begnoche, John P.
Beason‐Held, Lori L.
Shafer, Andrea T.
Resnick, Susan M.
Taylor, Warren D.
Price, Gavin R.
Morgan, Victoria L.
Rogers, Baxter P.
Schilling, Kurt G.
Landman, Bennett A. - Abstract:
- Abstract : Purpose: Diffusion weighted MRI imaging (DWI) is often subject to low signal‐to‐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. Conclusions: The proposed pipeline is a single integrated pipeline that combines established diffusion preprocessing tools from majorAbstract : Purpose: Diffusion weighted MRI imaging (DWI) is often subject to low signal‐to‐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. Conclusions: The proposed pipeline is a single integrated pipeline that combines established diffusion preprocessing tools from major MRI‐focused software packages with intuitive QA. … (more)
- Is Part Of:
- Magnetic resonance in medicine. Volume 86:Issue 1(2021)
- Journal:
- Magnetic resonance in medicine
- Issue:
- Volume 86:Issue 1(2021)
- Issue Display:
- Volume 86, Issue 1 (2021)
- Year:
- 2021
- Volume:
- 86
- Issue:
- 1
- Issue Sort Value:
- 2021-0086-0001-0000
- Page Start:
- 456
- Page End:
- 470
- Publication Date:
- 2021-02-03
- Subjects:
- denoising -- diffusion weighted imaging -- distortion correction -- DTI -- preprocessing -- quality assurance
Nuclear magnetic resonance -- Periodicals
Electron paramagnetic resonance -- Periodicals
616.07548 - Journal URLs:
- http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1522-2594 ↗
http://onlinelibrary.wiley.com/ ↗ - DOI:
- 10.1002/mrm.28678 ↗
- Languages:
- English
- ISSNs:
- 0740-3194
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - 5337.798000
British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 22919.xml