Ontario Neurodegenerative Disease Research Initiative (ONDRI): Structural MRI Methods and Outcome Measures

Abstract

The Ontario Neurodegenerative Research Initiative (ONDRI) is a 3 years multi-site prospective cohort study that has acquired comprehensive multiple assessment platform data, including 3T structural MRI, from neurodegenerative patients with Alzheimer's disease, mild cognitive impairment, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and cerebrovascular disease. This heterogeneous cross-section of patients with complex neurodegenerative and neurovascular pathologies pose significant challenges for standard neuroimaging tools. To effectively quantify regional measures of normal and pathological brain tissue volumes, the ONDRI neuroimaging platform implemented a semi-automated MRI processing pipeline that was able to address many of the challenges resulting from this heterogeneity. The purpose of this paper is to serve as a reference and conceptual overview of the comprehensive neuroimaging pipeline used to generate regional brain tissue volumes and neurovascular marker data that will be made publicly available online.

Cortical Thickness Estimation in Individuals With Cerebral Small Vessel Disease, Focal Atrophy, and Chronic Stroke Lesions

“…Incorporating more accurate brain extraction and lesion masks reduced the overall failure rate from 62% down to less than 8% when the corrected procedure was applied. This improvement could be attributed to the use of multi-modal imaging sequences in the ONDRI structural neuroimaging pipeline ( Ramirez et al, 2020 ) that produces consistent and accurate brain extraction and lesion segmentation. Although imaging markers of small vessel disease, such as WMH, appear hyperintense (bright) on PD/T2 and FLAIR MRI, these lesions appear hypointense or isointense to GM on T1, thus overlapping in intensity with normal appearing GM ( Wardlaw et al, 2013 ).…”

“…Magnetic resonance imaging protocols were harmonized with the Canadian Dementia Imaging Protocol (CDIP) ( Duchesne et al, 2019 ), and were in compliance with the National Institute of Neurological Disorders and Stroke–Canadian Stroke Network Vascular Cognitive Impairment Harmonization Standards ( Hachinski et al, 2006 ). Detailed MRI protocols are reported elsewhere ( Haddad et al, 2020 ; Ramirez et al, 2020 ). In brief, the structural MRI used in the current study include: a high-resolution 3D T1-weighted (T1), an interleaved proton density (PD) and T2-weighted (T2), and a T2 fluid-attenuated inversion recovery (FLAIR) images.…”

“…1 http://ondri.ca Ontario Neurodegenerative Disease Research Initiative's structural image processing pipeline (Ramirez et al, 2020) will be considered as the pre-processing step for the Corrected FS procedure. ONDRI's neuroimaging platform used previously published and validated methods, where outputs were further subjected to comprehensive quality control (QC) measures from ONDRI's neuroinformatic platform using a novel outlier detection algorithm for the identification of anomalous data (Beaton et al, 2019;Sunderland et al, 2019).…”

Multisite Comparison of MRI Defacing Software Across Multiple Cohorts

“…Since we were unable to collect photographs for the participants in the previous 300 scans, another, more recently-collected dataset was leveraged. Structural MRI scans using the ONDRI 3DT1 protocol ( 40 ) [scan parameters same as ( 28 )] were obtained from six participants (ages: 46–64, mean 56.5 years old) who participated in the OBI's Traveling Human Subject Study (THSS) and who gave consent to have their photographs and MRI renders to be used for this purpose. Three of these participants were personally familiar to the nine raters (mean familiarity 3.9 ± 5.7 years), while the remaining three participants were not familiar to the raters.…”

In vivo myelin imaging and tissue microstructure in white matter hyperintensities and perilesional white matter

“…Structural segmentation was performed with a previously published and validated segmentation and parcellation pipeline [28][29][30] . Briefly, T1, FLAIR, T2 and PD scans were linearly co-registered and supratentorial cerebral tissue was segmented into cerebrospinal fluid (CSF; sulcal and ventricular), grey matter, NAWM, and WMHs.…”