TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow &amp; Singularity

Theaud, Guillaume; Houde, Jean‐Christophe; Boré, Arnaud; Rheault, François; Morency, Félix C.; Descoteaux, Maxime

doi:10.1016/j.neuroimage.2020.116889

Cited by 128 publications

(134 citation statements)

References 53 publications

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“…Distortion, motion correction and estimation of non-linear transformations with the MNI space was performed using the HCP preprocessing pipelines [12]. Whole-brain tractograms were generated using the DIPY-based Tractoflow processing pipeline [46,47], producing both deterministic and probabilistic sets of streamlines to be given to participants. Importantly, to be as inclusive as possible to all definitions and constraints, streamlines were not filtered in any way.…”

Section: Data and Protocolmentioning

confidence: 99%

Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?

Schilling¹,

Rheault²,

Petit

et al. 2020

Preprint

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White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human wholebrain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process.

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Section: Data and Protocolmentioning

confidence: 99%

Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?

Schilling¹,

Rheault²,

Petit

et al. 2020

Preprint

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“…The diffusion-weighted images were processed using the TractoFlow Atlas-Based Segmentation (TractoFlow-ABS) pipeline. TractoFlow-ABS is an extension of the recent TractoFlow pipeline (Theaud et al, 2020a;Theaud et al, 2020b) publicly available for academic research purposes (https://github.com/scilus/tractoflow) that uses Nextflow (Di Tommaso et al, 2017) and Singularity (Kurtzer et al, 2017) to ensure efficient and reproducible diffusion processing. All major processing steps are performed through this pipeline, from preprocessing of the structural and diffusion images to tractography.…”

Section: Preprocessing Stepsmentioning

confidence: 99%

Bundle-specific associations between white matter microstructure and Aβ and tau pathology at their connecting cortical endpoints in older adults at risk of Alzheimer’s disease

Binette

Theaud

Rheault

et al. 2020

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Beta-amyloid (Aβ) and tau proteins, the pathological hallmarks of Alzheimer’s disease (AD), are believed to spread through connected regions. Combining diffusion imaging and positron emission tomography, we investigated associations between Aβ, tau and white matter microstructure specifically in bundles connecting brain regions in which AD pathology accumulates. In 126 cognitively normal elderly at risk of AD, we focussed on free-water corrected diffusion measures in the cingulum, posterior cingulum, fornix and uncinate fasciculus. We found higher tissue fractional anisotropy and lower mean and radial diffusivity related to increased Aβ at the cortical endpoints of the cingulum and fornix. We observed similar but stronger associations in the uncinate fasciculus, but with increased Aβ and tau at the endpoints of this bundle. This consistent pattern of associations, with opposite directionality to the usual degeneration pattern in symptomatic individuals, suggests more restricted diffusion in bundles vulnerable to preclinical AD pathology.

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“…TractoFlow-ABS is based on TractoFlow [Theaud et al, 2020]. The graph of processes of the TractoFlow-ABS pipeline.…”

Section: Methodsmentioning

confidence: 99%

“…Diffusion-weighted images (DWI) tasks. The DWI tasks are the same as presented in the original TractoFlow paper [Theaud et al, 2020]. The steps are illustrated in Figure 1.B.…”

Section: Methodsmentioning

confidence: 99%

“…In the field of diffusion MRI, these lesions can affect DWI processing and more precisely the tractography step [Edde et al, 2019;Theaud et al, 2017]. In order to do the best processing as possible, a version of TractoFlow [Theaud et al, 2020] was developed for brains where the usual T1 segmentation step fails. Compared to TractoFlow, TractoFlow-ABS uses Freesurfer to compute tissue masks instead of fast from FSL.…”

Section: Introductionmentioning

confidence: 99%

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TractoFlow-ABS (Atlas-Based Segmentation)

Theaud

Houde

Boré

et al. 2020

Preprint

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TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity

Cited by 128 publications

References 53 publications

Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?

Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?

Bundle-specific associations between white matter microstructure and Aβ and tau pathology at their connecting cortical endpoints in older adults at risk of Alzheimer’s disease

TractoFlow-ABS (Atlas-Based Segmentation)

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