MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation

Tournier, Jacques‐Donald; Smith, Robert E.; Raffelt, David; Tabbara, Rami; Dhollander, Thijs; Pietsch, Maximilian; Christiaens, Daan; Jeurissen, Ben; Yeh, Chun‐Hung; Connelly, Alan

doi:10.1016/j.neuroimage.2019.116137

Cited by 1,765 publications

(1,533 citation statements)

References 48 publications

(49 reference statements)

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“…To calculate fixel-based metrics we utilized the b=1000s/mm 2 DWIs and generally followed the MRtrix3 (Tournier et al, 2019) (https://www.mrtrix.org/) FBA processing pipeline 1 (Raffelt et al, 2017b), with the exception that instead of using the standard constrained spherical deconvolution approach (Tournier et al, 2007) estimation of white matter fiber orientation distributions (FODs) was done for each participant via "single-shell 3-tissue constrained spherical deconvolution" (SS3T-CSD) using a group averaged response function for each tissue type (white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF)) Raffelt et al, 2012b). This step was performed using MRtrix3Tissue (https://3tissue.github.io/), a fork of MRtrix3 (Tournier et al, 2019).…”

Section: Fba and Fixel Metricsmentioning

confidence: 99%

Early childhood development of white matter fiber density and morphology

Dimond

Rohr

Smith

et al. 2019

Preprint

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Early childhood is an important period for cognitive and brain development, though white matter changes specific to this period remain understudied. Here we utilize a novel analytic approach to quantify and track developmental changes in white matter micro-and macro-structure, calculated from individually oriented fiber-bundle populations, termed "fixels". Fixel-based analysis and mixed-effects models were used to assess tract-wise changes in fiber density and bundle morphology in 73 girls scanned at baseline (ages 4.09-7.02, mean=5.47, SD=0.81), 6-month (N=7), and one-year follow-up (N=42). For comparison, we also assessed changes in commonly utilized diffusion tensor metrics: fractional anisotropy (FA), and mean, radial and axial diffusivity (MD, RD, AD). Maturational increases in fixel-metrics were seen in most major white matter tracts, with the most rapid increases in the corticospinal tract and slowest or non-significant increases in the genu of the corpus callosum and uncinate fasciculi. As expected, we observed developmental increases in FA and decreases in MD, RD and AD, though percentage changes were smaller relative to fixel-metrics. The majority of tracts showed more substantial morphological than microstructural changes. These findings highlight early childhood as a period of dynamic white matter maturation, characterized by large increases in macroscopic fiber bundle size, mild changes in axonal density, and parallel, albeit less substantial, changes in diffusion tensor metrics.

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Section: Fba and Fixel Metricsmentioning

confidence: 99%

Early childhood development of white matter fiber density and morphology

Dimond

Rohr

Smith

et al. 2019

Preprint

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“…We used this comprehensive, combinatorial approach because specific choices at one stage may interact with choices at other stages. The steps that we focused on are featured prominently in preprocessing pipelines that are implemented as part of the FSL (Jenkinson, Beckmann, Behrens, Woolrich, & Smith, 2012) and MRtrix3 (Tournier et al, 2019) software packages. From FSL, we rely on the preprocessing tools topup and eddy (Jenkinson et al, 2012), which provide estimation of B0 field inhomogeneities (Andersson, Skare, & Ashburner, 2003; S. M. Smith et al, 2004), and correction for these distortions in addition to correction for motion, eddy current distortions, and signal dropout (Andersson et al, 2017, respectively.…”

Section: Overviewmentioning

confidence: 99%

“…From FSL, we rely on the preprocessing tools topup and eddy (Jenkinson et al, 2012), which provide estimation of B0 field inhomogeneities (Andersson, Skare, & Ashburner, 2003; S. M. Smith et al, 2004), and correction for these distortions in addition to correction for motion, eddy current distortions, and signal dropout (Andersson et al, 2017, respectively. From MRtrix3, we relied on the standard workflow for connectome construction Tournier et al, 2019), due to the availability of many different relevant preprocessing algorithms and choices thereof, particularly those designed to optimize connectomic measures. We focus on these steps and packages because they are commonly used in connectome construction and include many relevant preprocessing choices in a simple workflow.…”

Section: Overviewmentioning

confidence: 99%

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The efficacy of different preprocessing steps in reducing motion-related confounds in diffusion MRI connectomics

Oldham

Arnatkevičiūtė

Smith

et al. 2020

Preprint

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Head motion is a major confounding factor in neuroimaging studies. While numerous studies have investigated how motion impacts estimates of functional connectivity, the effects of motion on structural connectivity measured using diffusion MRI have not received the same level of attention, despite the fact that, like functional MRI, diffusion MRI relies on elaborate preprocessing pipelines that require multiple choices at each step. Here, we report a comprehensive analysis of how these choices influence motion-related contamination of structural connectivity estimates. Using a healthy adult sample (N = 252), we evaluated 240 different preprocessing pipelines, devised using plausible combinations of different choices related to explicit head motion correction, tractography propagation algorithms, track seeding methods, track termination constraints, quantitative metrics derived for each connectome edge, and parcellations. We found that an approach to motion correction that includes outlier replacement and within-slice volume correction led to a dramatic reduction in cross-subject correlations between head motion and structural connectivity strength, and that motion contamination is more severe when quantifying connectivity strength using mean tract fractional anisotropy rather than streamline count. We also show that the choice of preprocessing strategy can significantly influence subsequent inferences about network organization, with the location of network hubs varying considerably depending on the specific preprocessing steps applied. Our findings indicate that the impact of motion on structural connectivity can be successfully mitigated using recent motion-correction algorithms that include outlier replacement and within-slice motion correction.HighlightsWe assess how motion affects structural connectivity in 240 preprocessing pipelinesMotion contamination of structural connectivity depends on preprocessing choicesAdvanced motion correction tools reduce motion confoundsFA edge weighting is more susceptible to motion effects than streamline count

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“…Whole-heart 4D flow cine volumes for each subject were assessed by an expert MRI fetal cardiologist (DL) using MRtrix3 31 Figure 9a shows blood flow curves from fetus ID03 (healthy, GA 24 +4 ). When taking the mean of the entire cohort (n = 7, Figure 9b), blood flow values were lower than expected from literature, by approximately a factor of 2 depending on the vessel.…”

Section: Evaluation Of 4d Flow Cine Volumesmentioning

confidence: 99%

Fetal whole-heart 4D flow cine MRI using multiple non-coplanar balanced SSFP stacks

Roberts

Amerom

Uus

et al. 2019

Preprint

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Purpose:To develop an MRI framework for reconstruction of 4D velocity vector blood flow volumes for visualisation and quantification of circulation in the fetal heart and major vessels. Methods:A novel method of velocity-encoding using multiple non-coplanar stacks of bSSFP phase images was combined with a previous framework for reconstruction of motioncorrected 4D magnitude cine volumes to generate spatiotemporally-paired 4D flow cine volumes of the fetal circulatory system. The multiple stack velocity-encoding scheme was validated in a simulated flow phantom and compared with a gold-standard method for velocity-encoding in a physical flow phantom. The 4D flow cine framework was evaluated in seven fetal subjects. Reconstructed 4D flow volumes were evaluated by an expert fetal cardiologist and preliminary flow measurements were taken in various major vessels of the heart. Results:Phantom experiments showed that the multiple non-coplanar stack velocityencoding scheme was accurate. The 4D flow cine reconstruction framework was robust in fetal subjects and generated multi-dimensional velocity vector maps of blood flow through the cardiac cycle. Directionality of blood flow was consistent with expected fetal circulatory hemodynamics. Relative blood flow rates in the major vessels were in line with previous observations, although absolute values were underestimated by a factor of approximately two due to limitations of spatial and temporal resolution.Conclusion: 4D flow cine volumes can be reconstructed from multiple non-coplanar stacks of slices. The proposed framework was used to visualise and quantify flow through the whole fetal heart and great vessels, but is applicable to any imaging scenario where motion is a major challenge.

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MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation

Cited by 1,765 publications

References 48 publications

Early childhood development of white matter fiber density and morphology

Early childhood development of white matter fiber density and morphology

The efficacy of different preprocessing steps in reducing motion-related confounds in diffusion MRI connectomics

Fetal whole-heart 4D flow cine MRI using multiple non-coplanar balanced SSFP stacks

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