<b>TractoR</b>: Magnetic Resonance Imaging and Tractography with<i>R</i>

Clayden, Jonathan D.; Maniega, Susana Muñoz; Storkey, Amos; King, Martin D.; Bastin, Mark E.; Clark, Chris A.

doi:10.18637/jss.v044.i08

Cited by 95 publications

(95 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…28 DT-MR images were processed using in-house software, which removed bulk motion and eddy current induced distortions using FSL FLIRT and generated a directionally averaged diffusion weighted image, MD and FA parametric images using standard methods based on multivariate linear regression. For each dataset, non-linear registration tools from the TractoR software package (www.tractor-mri.org.uk/diffusionprocessing) 29,30 were used to obtain the transformation between the brain extracted structural T2W image and the b0 diffusion volume.…”

Section: Image Processingmentioning

confidence: 99%

Integrity of normal-appearing white matter: Influence of age, visible lesion burden and hypertension in patients with small-vessel disease

Maniega

Chappell

Hernández

et al. 2016

J Cereb Blood Flow Metab

150

131

View full text Add to dashboard Cite

White matter hyperintensities accumulate with age and occur in patients with stroke, but their pathogenesis is poorly understood. We measured multiple magnetic resonance imaging biomarkers of tissue integrity in normal-appearing white matter and white matter hyperintensities in patients with mild stroke, to improve understanding of white matter hyperintensities origins. We classified white matter into white matter hyperintensities and normal-appearing white matter and measured fractional anisotropy, mean diffusivity, water content (T1-relaxation time) and blood-brain barrier leakage (signal enhancement slope from dynamic contrast-enhanced magnetic resonance imaging). We studied the effects of age, white matter hyperintensities burden (Fazekas score) and vascular risk factors on each biomarker, in normalappearing white matter and white matter hyperintensities, and performed receiver-operator characteristic curve analysis. Amongst 204 patients (34.3-90.9 years), all biomarkers differed between normal-appearing white matter and white matter hyperintensities (P < 0.001). In normal-appearing white matter and white matter hyperintensities, mean diffusivity and T1 increased with age (P < 0.001), all biomarkers varied with white matter hyperintensities burden (P < 0.001; P ¼ 0.02 signal enhancement slope), but only signal enhancement slope increased with hypertension (P ¼ 0.028). Fractional anisotropy showed complex age-white matter hyperintensities-tissue interactions; enhancement slope showed white matter hyperintensities-tissue interactions. Mean diffusivity distinguished white matter hyperintensities from normal-appearing white matter best at all ages. Blood-brain barrier leakage increases with hypertension and white matter hyperintensities burden at all ages in normal-appearing white matter and white matter hyperintensities, whereas water mobility and content increase as tissue damage accrues, suggesting that blood-brain barrier leakage mediates small vessel disease-related brain damage.

show abstract

Section: Image Processingmentioning

confidence: 99%

Integrity of normal-appearing white matter: Influence of age, visible lesion burden and hypertension in patients with small-vessel disease

Maniega

Chappell

Hernández

et al. 2016

J Cereb Blood Flow Metab

150

131

View full text Add to dashboard Cite

show abstract

“…The DTI data were preprocessed using TractoR version 2.3 24 and FMRIB Software Library version 5.0. 21 Within each subject, a reference b=0 volume was brain extracted, and diffusionweighted volumes were registered to this volume to correct for eddy current distortions.…”

Section: Dti Preprocessingmentioning

confidence: 99%

White Matter Damage Relates to Oxygen Saturation in Children With Sickle Cell Anemia Without Silent Cerebral Infarcts

Kawadler

Kirkham

Clayden

et al. 2015

Stroke

Self Cite

View full text Add to dashboard Cite

Background and Purpose-Sickle cell anemia is associated with compromised oxygen-carrying capability of hemoglobin and a high incidence of overt and silent stroke. However, in children with no evidence of cerebral infarction, there are changes in brain morphometry relative to healthy controls, which may be related to chronic anemia and oxygen desaturation. Methods-A whole-brain tract-based spatial statistics analysis was carried out in 25 children with sickle cell anemia with no evidence of abnormality on T2-weighted magnetic resonance imaging (13 male, age range: 8-18 years) and 14 age-and race-matched controls (7 male, age range: 10-19 years) to determine the extent of white matter injury. The hypotheses that white matter damage is related to daytime peripheral oxygen saturation and steady-state hemoglobin were tested. Results-Fractional anisotropy was found to be significantly lower in patients in the subcortical white matter (corticospinal tract and cerebellum), whereas mean diffusivity and radial diffusivity were higher in patients in widespread areas. There was a significant negative relationship between radial diffusivity and oxygen saturation (P<0.05) in the anterior corpus callosum and a trend-level negative relationship between radial diffusivity and hemoglobin (P<0.1) in the midbody of the corpus callosum. Conclusions-These data show widespread white matter abnormalities in a sample of asymptomatic children with sickle cell anemia, and provides for the first time direct evidence of a relationship between brain microstructure and markers of disease severity (eg, peripheral oxygen saturation and steady-state hemoglobin). This study suggests that diffusion tensor imaging metrics may serve as a biomarker for future trials of reducing hypoxic exposure. (Stroke. 2015;46:1793-1799.

show abstract

“…The two sets of PNT standard reference tracts are available through the TractoR (Tractography with R) project (http://www.tractor-mri.org.uk/) [27]. These represent most of the main pathways in the brain, as described by Hua et al [17].…”

Section: Reference Tractsmentioning

confidence: 99%

Reference Tracts and Generative Models for Brain White Matter Tractography

et al. 2017

View full text Add to dashboard Cite

Background: Probabilistic neighborhood tractography aims to automatically segment brain white matter tracts from diffusion magnetic resonance imaging (dMRI) data in different individuals. It uses reference tracts as priors for the shape and length of the tract, and matching models that describe typical deviations from these. We evaluated new reference tracts and matching models derived from dMRI data acquired from 80 healthy volunteers, aged 25-64 years. Methods: The new reference tracts and models were tested in 50 healthy older people, aged 71.8 ± 0.4 years. The matching models were further assessed by sampling and visualizing synthetic tracts derived from them. Results: We found that data-generated reference tracts improved the success rate of automatic white matter tract segmentations. We observed an increased rate of visually acceptable tracts, and decreased variation in quantitative parameters when using this approach. Sampling from the matching models demonstrated their quality, independently of the testing data. Conclusions: We have improved the automatic segmentation of brain white matter tracts, and demonstrated that matching models can be successfully transferred to novel data. In many cases, this will bypass the need for training data and make the use of probabilistic neighborhood tractography in small testing datasets newly practicable.

show abstract

TractoR: Magnetic Resonance Imaging and Tractography withR

Cited by 95 publications

References 13 publications

Integrity of normal-appearing white matter: Influence of age, visible lesion burden and hypertension in patients with small-vessel disease

Integrity of normal-appearing white matter: Influence of age, visible lesion burden and hypertension in patients with small-vessel disease

White Matter Damage Relates to Oxygen Saturation in Children With Sickle Cell Anemia Without Silent Cerebral Infarcts

Reference Tracts and Generative Models for Brain White Matter Tractography

Contact Info

Product

Resources

About