An overview of the quality assurance and quality control of magnetic resonance imaging data for the Ontario Neurodegenerative Disease Research Initiative (ONDRI): pipeline development and neuroinformatics

Abstract

Large scale research studies combining magnetic resonance imaging data generated at multiple sites on multiple vendor platforms are becoming more commonplace. The Ontario Neurodegenerative Disease Research Initiative (ONDRI -http://ondri.ca/), a project funded by the Ontario Brain Institute (OBI), is a recently established province-wide natural history study, which has recruited more than 500 participants from neurodegenerative disease groups including amyotrophic lateral sclerosis, fronto-temporal dementia, Parkinson's disease, Alzheimer's disease, mild cognitive impairment, and cerebrovascular disease (previously referred to as the vascular cognitive impairment cohort). Because of its multi-site nature, all captured data must be standardized and meet minimum quality standards to reduce variability. The goal of the ONDRI imaging platform is to maximize data quality by implementing vendor-specific harmonized MR imaging protocols (consistent with the Canadian Dementia Imaging Protocol -http://www.cdip-pcid.ca/), monitoring protocol adherence, qualitatively assessing image quality, measuring signal-to-noise and contrast-to-noise, monitoring system stability, and applying corrections based on the analysis of images from two different phantoms regularly acquired at each site. To maximize image quality, this work describes the use of various automatic pipelines and manual assessment steps, integrated within an established informatics and databasing platform, the Stroke Patient Recovery Research Database (SPReD) built on the Extensible Neuroimaging Archive Toolkit (XNAT), and contained within the Brain-CODE (Centre for Ontario Data Exploration) framework. The purpose of the current paper is to describe the steps undertaken by ONDRI to achieve this high standard of data integrity. Data have been successfully collected for the past 4 years with the pipelines and assessments identifying deviations, allowing for timely interventions and assessment of image quality.

Visual QC Protocol for FreeSurfer Cortical Parcellations from Anatomical MRI

“…We analyzed two large multi-site datasets that were drawn from previous studies 1) the Canadian Biomarker Integration Network in Depression (CAN-BIND) with 308 participants (MacQueen et al 2019;Lam et al 2016), and 2) the Parkinson's disease cohort from the Ontario Neurodegeneration Research Initiative (ONDRI) (Farhan et al 2017;Scott et al 2020), with 140 participants with Parkinson's Disease. Demographic information of the two datasets are shown in Table 1.…”

The Ontario Neurodegenerative Disease Research Initiative

“…To account for the more rapid motoric and respiratory decline of individuals with ALS, participants in that cohort completed clinical, neuropsychology, and eye tracking assessments at 6-month intervals. Additional information pertaining to the assessment platforms is provided elsewhere 11,[24][25][26][27][28][29][30][31] .…”

“…All data are stored in Brain-CODE 33 : a secure, centralized neuroinformatics system designed for the collection, storage, federation, sharing, and analysis of different types of data using a diverse set of electronic data capture tools including XNAT, RedCap, and LabKey. Rigorous, assessment-specific data pre-processing and quality control procedures were developed and executed to ensure data were of the highest-possible fidelity [26][27][28][29][30][31] . This included investigation of any missing data and the use of detailed, non-numeric missing codes to indicate broad categories for missing values where they could be determined.…”

“…ONDRI data underwent extensive cleaning and quality control pipelines to identify and correct data entry or processing errors [26][27][28][29][30][31] , or document anomalies 34 , thereby increasing the accuracy and integrity of data and consequently reducing the risk of incorrect conclusions. While such protocols can be time consuming, they serve a two-fold benefit: more accurate results due to correction of erroneously recorded data and more nuanced analyses sensitive to idiosyncrasies in the sample.…”

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

“…The Ontario Neurodegenerative Research Initiative (ONDRI) is a multi-site prospective cohort study following patients with neurodegenerative diseases including Alzheimer's disease (AD), mild cognitive impairment (MCI), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and cerebrovascular disease (CVD). Over the course of 3 years, multiple assessment platforms acquired comprehensive data from the 520 patients including: neuroimaging ( 1 – 3 ), clinical and demographic assessments ( 4 ), neuropsychology ( 5 ), genetic variations ( 6 , 7 ), eye tracking and pupillometry, retinal layer analyses using spectral-domain optical coherence tomography ( 8 ), gait and balance performance ( 9 ), and neuropathology. The multi-modal data collected from ONDRI will be used to explore earlier detection, guide development of novel therapy, and improve patient care.…”