Cited by 827Advanced Neuroimaging Techniques and ApplicationsAdvanced MRI Techniques and ApplicationsFunctional Brain Connectivity Studies

Twenty‐five pitfalls in the analysis of diffusion MRI data

Open access
Jones, Derek K., Cercignani, Mara·2010·NMR in Biomedicine

Abstract

Obtaining reliable data and drawing meaningful and robust inferences from diffusion MRI can be challenging and is subject to many pitfalls. The process of quantifying diffusion indices and eventually comparing them between groups of subjects and/or correlating them with other parameters starts at the acquisition of the raw data, followed by a long pipeline of image processing steps. Each one of these steps is susceptible to sources of bias, which may not only limit the accuracy and precision, but can lead to substantial errors. This article provides a detailed review of the steps along the analysis pipeline and their associated pitfalls. These are grouped into pre‐processing of data; estimation of the tensor; derivation of voxelwise quantitative parameters; strategies for extracting quantitative parameters; and finally intra‐subject and inter‐subject comparison, including region of interest, histogram, tract‐specific and voxel‐based analyses. The article covers important aspects of diffusion MRI analysis, such as motion correction, susceptibility and eddy current distortion correction, model fitting, region of interest placement, histogram and voxel‐based analysis. We have assembled 25 pitfalls (several previously unreported) into a single article, which should serve as a useful reference for those embarking on new diffusion MRI‐based studies, and as a check for those who may already be running studies but may have overlooked some important confounds. While some of these problems are well known to diffusion experts, they might not be to other researchers wishing to undertake a clinical study based on diffusion MRI. Copyright © 2010 John Wiley & Sons, Ltd.

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Crossref · 10.1002/nbm.1543

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  • Even in regions with crossing fibers, many observed differences or changes in FA, AD and/or RD are likely to reflect actual anatomical and biophysical phenomena, as long as other pitfalls in acquisition and analysis have been avoided.

    “as pointed out by Jeurissen et al. (2013), even regions with crossing fibers, many observed differences/changes in FA, AD and/or RD are likely to reflect actual anatomical and biophysical phenomena, as long as other pitfalls in the acquisition and analysis have been avoided (Jones and Cercignani, 2010).”
  • DTI based tractography has difficulties in resolving fibre tracking in areas with mixed fibre orientations due to, for instance, intra-voxel fibre crossing.

    “While DTI based tractography (Basser et al., 2000) has been widely applied, it has difficulties in resolving fibre tracking in areas with mixed fibre orientations due to, for instance, intra-voxel fibre crossing (Jones and Cercignani, 2010; Jeurissen et al., 2017).”

    From The cingulum bundle: Anatomy, function, and dysfunction (2018) · cites this paper as Jones and Cercignani, 2010

  • The interpretation of diffusion data is hampered by limitations, primary among which is a lack of understanding of the actual biological sources underlying widely used DTI-derived measures.

    “While DTI has provided extraordinary insights into the WM structure of the brain in both health and disease, the interpretation of diffusion data is often hampered by several important limitations and challenges (Beaulieu, 2002; Jones and Cercignani, 2010). Primary among these limitations is a lack of understanding of the actual biological sources underlying widely used DTI-derived measures.”
  • Diffusion-weighted imaging has many limitations and sources of error at each step of the analysis pipeline.

    “Moreover, diffusion-weighted imaging has many limitations and sources of error at each step of the analysis pipeline that must be considered when interpreting results236, 237.”

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Authors
Jones, D. K., & Cercignani, M.
Affiliations
  • Cardiff University (GB)
  • Fondazione Santa Lucia (IT)
Corresponding author
Jones, Derek K.
Venue
NMR in Biomedicine
Publisher
Wiley
Published
2010-08
Volume
23
Issue
7
Pages
803-820
ISSN
  • 0952-3480 (ISSN-L)
  • 1099-1492
OpenAlex
W2015391962
Cited by
827
References
71
Citations by year
2026: 36 · 2025: 27 · 2024: 36 · 2023: 40 · 2022: 51 · 2021: 51 · 2020: 52 · 2019: 56 · 2018: 51 · 2017: 72 · 2016: 63 · 2015: 79 · 2014: 68 · 2013: 60 · 2012: 51
FWCI
6.57
Type
journal article
Language
en
Open access
Locations
  • NMR in Biomedicine (publishedVersion)
  • PubMed (publishedVersion)
  • Figshare (submittedVersion, cc-by)
Topics
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
  • Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
Keywords
diffusion MRI, eddy current correction, susceptibility distortion correction, motion correction, diffusion tensor estimation, model fitting, region of interest placement, voxel-based analysis, histogram analysis, diffusion indices
MeSH terms
Algorithms, Brain, Cerebrospinal Fluid, Humans, Image Enhancement, Image Processing, Computer-Assisted, Artifacts, Diffusion Magnetic Resonance Imaging

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