David F. Tate

YNICL Journal 2024 Journal Article

ENIGMA’s simple seven: Recommendations to enhance the reproducibility of resting-state fMRI in traumatic brain injury

• Karen Caeyenberghs
• Phoebe Imms
• Andrei Irimia
• Martin M. Monti
• Carrie Esopenko
• Nicola L. de Souza
• Juan F. Dominguez D
• Mary R. Newsome

Resting state functional magnetic resonance imaging (rsfMRI) provides researchers and clinicians with a powerful tool to examine functional connectivity across large-scale brain networks, with ever-increasing applications to the study of neurological disorders, such as traumatic brain injury (TBI). While rsfMRI holds unparalleled promise in systems neurosciences, its acquisition and analytical methodology across research groups is variable, resulting in a literature that is challenging to integrate and interpret. The focus of this narrative review is to address the primary methodological issues including investigator decision points in the application of rsfMRI to study the consequences of TBI. As part of the ENIGMA Brain Injury working group, we have collaborated to identify a minimum set of recommendations that are designed to produce results that are reliable, harmonizable, and reproducible for the TBI imaging research community. Part one of this review provides the results of a literature search of current rsfMRI studies of TBI, highlighting key design considerations and data processing pipelines. Part two outlines seven data acquisition, processing, and analysis recommendations with the goal of maximizing study reliability and between-site comparability, while preserving investigator autonomy. Part three summarizes new directions and opportunities for future rsfMRI studies in TBI patients. The goal is to galvanize the TBI community to gain consensus for a set of rigorous and reproducible methods, and to increase analytical transparency and data sharing to address the reproducibility crisis in the field.

YNICL Journal 2013 Journal Article

Disrupted cerebral metabolite levels and lower nadir CD4 + counts are linked to brain volume deficits in 210 HIV-infected patients on stable treatmentpatients on stable treatment

• Xue Hua
• Christina P. Boyle
• Jaroslaw Harezlak
• David F. Tate
• Constantin T. Yiannoutsos
• Ron Cohen
• Giovanni Schifitto
• Assawin Gongvatana

Cognitive impairment and brain injury are common in people with HIV/AIDS, even when viral replication is effectively suppressed with combined antiretroviral therapies (cART). Metabolic and structural abnormalities may promote cognitive decline, but we know little about how these measures relate in people on stable cART. Here we used tensor-based morphometry (TBM) to reveal the 3D profile of regional brain volume variations in 210 HIV + patients scanned with whole-brain MRI at 1.5 T (mean age: 48.6 ± 8.4 years; all receiving cART). We identified brain regions where the degree of atrophy was related to HIV clinical measures and cerebral metabolite levels assessed with magnetic resonance spectroscopy (MRS). Regional brain volume reduction was linked to lower nadir CD4 + count, with a 1-2% white matter volume reduction for each 25-point reduction in nadir CD4 +. Even so, brain volume measured by TBM showed no detectable association with current CD4 + count, AIDS Dementia Complex (ADC) stage, HIV RNA load in plasma or cerebrospinal fluid (CSF), duration of HIV infection, antiretroviral CNS penetration-effectiveness (CPE) scores, or years on cART, after controlling for demographic factors, and for multiple comparisons. Elevated glutamate and glutamine (Glx) and lower N-acetylaspartate (NAA) in the frontal white matter, basal ganglia, and mid frontal cortex - were associated with lower white matter, putamen and thalamus volumes, and ventricular and CSF space expansion. Reductions in brain volumes in the setting of chronic and stable disease are strongly linked to a history of immunosuppression, suggesting that delays in initiating cART may result in imminent and irreversible brain damage.

YNIMG Journal 2011 Journal Article

Stochastic tractography study of Inferior Frontal Gyrus anatomical connectivity in schizophrenia

• Marek Kubicki
• Jorge L. Alvarado
• Carl-Fredrik Westin
• David F. Tate
• Douglas Markant
• Douglas P. Terry
• Thomas J. Whitford
• Julien De Siebenthal

Background Abnormalities within language-related anatomical structures have been associated with clinical symptoms and with language and memory deficits in schizophrenia. Recent studies suggest disruptions in functional connectivity within the Inferior Frontal Gyrus (IFG) network in schizophrenia. However, due to technical challenges, anatomical connectivity abnormalities within this network and their involvement in clinical and cognitive deficits have not been studied. Material and methods Diffusion and anatomical scans were obtained from 23 chronic schizophrenia patients and 23 matched controls. The IFG was automatically segmented, and its white matter connections extracted and measured with newly-developed stochastic tractography tools. Correlations between anatomical structures and measures of semantic processing were also performed. Results White Matter connections between the IFG and posterior brain regions followed two distinct pathways: dorsal and ventral. Both demonstrated left lateralization, but ventral pathway abnormalities were only found in schizophrenia. IFG volumes also showed left lateralization and abnormalities in schizophrenia. Further, despite similar laterality and abnormality patterns, IFG volumes and white matter connectivity were not correlated with each other in either group. Interestingly, measures of semantic processing correlated with white matter connectivity in schizophrenia and with gray matter volumes in controls. Finally, hallucinations were best predicted by both gray matter and white matter measures together. Conclusions Our results suggest abnormalities within the ventral IFG network in schizophrenia, with white matter abnormalities better predicting semantic deficits. The lack of a statistical relationship between coexisting gray and white matter deficits might suggest their different origin and the necessity for a multimodal approach in future schizophrenia studies.

YNIMG Journal 2010 Journal Article

Reliability and validity of MRI-based automated volumetry software relative to auto-assisted manual measurement of subcortical structures in HIV-infected patients from a multisite study

• Jeffrey Dewey
• George Hana
• Troy Russell
• Jared Price
• Daniel McCaffrey
• Jaroslaw Harezlak
• Ekta Sem
• Joy C. Anyanwu

The automated volumetric output of FreeSurfer and Individual Brain Atlases using Statistical Parametric Mapping (IBASPM), two widely used and well published software packages, was examined for accuracy and consistency relative to auto-assisted manual (AAM) tracings (i. e. , manual correction of automated output) when measuring the caudate, putamen, amygdala, and hippocampus in the baseline scans of 120 HIV-infected patients (86. 7% male, 47. 3±6. 3y. o. , mean HIV duration 12. 0±6. 3years) from the NIH-funded HIV Neuroimaging Consortium (HIVNC) cohort. The data was examined for accuracy and consistency relative to auto-assisted manual tracing, and construct validity was assessed by correlating automated and AAM volumetric measures with relevant clinical measures of HIV progression. When results were averaged across all patients in the eight structures examined, FreeSurfer achieved lower absolute volume difference in five, higher sensitivity in seven, and higher spatial overlap in all eight structures. Additionally, FreeSurfer results exhibited less variability in all measures. Output from both methods identified discrepant correlations with clinical measures of HIV progression relative to AAM segmented data. Overall, FreeSurfer proved more effective in the context of subcortical volumetry in HIV-patients, particularly in a multisite cohort study such as this. These findings emphasize that regardless of the automated method used, visual inspection of segmentation output, along with manual correction if necessary, remains critical to ensuring the validity of reported results.

YNIMG Journal 2009 Journal Article

Corrigendum to “Quantitative tractography metrics of white matter integrity in diffusion-tensor MRI” [NeuroImage 42 (2008) 568–581]

• Stephen Correia
• Stephanie Y. Lee
• Thom Voorn
• David F. Tate
• Robert H. Paul
• Song Zhang
• Stephen P. Salloway
• Paul F. Malloy

YNIMG Journal 2008 Journal Article

Quantitative tractography metrics of white matter integrity in diffusion-tensor MRI

• Stephen Correia
• Stephanie Y. Lee
• Thom Voorn
• David F. Tate
• Robert H. Paul
• Song Zhang
• Stephen P. Salloway
• Paul F. Malloy

We present new quantitative diffusion-tensor imaging (DTI) tractography-based metrics for assessing cerebral white matter integrity. These metrics extend prior work in this area. Tractography models of cerebral white matter were produced from each subject's DTI data. The models are a set of curves (e. g. , “streamtubes”) derived from DTI data that represent the underlying topography of the cerebral white matter. Nine metrics were calculated in whole brain tractography models and in three “tracts-of-interest”: transcallosal fibers and the left and right cingulum bundles. The metrics included the number of streamtubes and several other based on the summed length of streamtubes, including some that were weighted by scalar anisotropy metrics and normalized for estimated intracranial volume. We then tested whether patients with subcortical ischemic vascular disease (i. e. , vascular cognitive impairment or VCI) vs. healthy controls (HC) differed on the metrics. The metrics were significantly lower in the VCI group in whole brain and in transcallosal fibers but not in the left or right cingulum bundles. The metrics correlated significantly with cognitive functions known to be impacted by white matter abnormalities (e. g. , processing speed) but not with those more strongly impacted by cortical disease (e. g. , naming). These new metrics help bridge the gap between DTI tractography and scalar analytical methods and provide a potential means for examining group differences in white matter integrity in specific tracts-of-interest.