FreeSurfer based cortical mapping and T1-relaxometry with MPnRAGE: Test-retest reliability with and without retrospective motion correction

Abstract

A test-retest study of FreeSurfer derived cortical thickness, cortical surface area, and cortical volume, as well as quantitative R1 relaxometry assessed on the midpoint of the cortex, was performed on a cohort of pediatric subjects (6–12 years old) scanned without sedation using SNARE-MPnRAGE ( s elf na vigated re trospective motion corrected m agnetization p repared with n r apid g radient e choes) imaging. Reliability was assessed with coefficients of variation (CoVs) and intraclass correlation coefficients (ICCs) and statistical tests were used to determine differences with and without SNARE motion correction. Comparison of the test-retest measures of SNARE-MPnRAGE with prospectively motion corrected PROMO MPRAGE were also performed. When SNARE motion correction was used all parameters had statistically significant improvements and demonstrated high reliability. Reliability varied depending on parameter, region, and measurement type (vertex or region of interest). For mean thickness/surface area/volume/mean R1 across the regions of FreeSurfer’s DK Atlas, the mean CoVs (% x100) were (1.2/1.6/1.9/0.9) and the mean ICCs were (0.88/0.96/0.94/0.83). When assessed on a per-vertex basis, the CoVs and ICCs for thickness/R1 had mean values of (2.9/1.9) and (0.82/0.68) across the regions of the DK Atlas. Retrospectively motion corrected MPnRAGE had significantly lower CoVs and higher ICCs for the morphological measures than PROMO MPRAGE. Motion correction effectively removed motion related biases in nearly all regions for R1 and morphometric measures.

Validation of cross-sectional and longitudinal ComBat harmonization methods for magnetic resonance imaging data on a travelling subject cohort

“…The scan-rescan variability observed in our study, both within and across scanners, compares well with those previously reported for volumes ( Wittens et al, 2021 ; De Guio et al, 2016 ; Jovicich et al, 2009 ; Kruggel et al, 2010 ; Yang et al, 2016 ; Fujita et al, 2019 ; Vavasour et al, 2019 ; Deprez et al, 2018 ), cortical thickness ( Fujita et al, 2019 ; Kecskemeti et al, 2021 ; Mcguire et al, 2017 ) and diffusion metrics ( Acheson et al, 2017 ; Grech‐Sollars et al, 2015 ; Kamagata et al, 2015 ; Liu et al, 2014 ; Palacios et al, 2017 ; Prohl et al, 2019 ; Shahim et al, 2017 ; Veenith et al, 2013 ; Zhou et al, 2018 ).…”

Role of autonomic, nociceptive, and limbic brainstem nuclei in core autism features

“…Additionally, quantitative T1 (qT1) maps were used to generate R1 estimations (R1 = 1/qT1) at each voxel using MPnRAGE images (Kecskemeti et al, 2021). While R1 can be influenced by several biological factors, it is often associated with the presence of myelination (Dick et al, 2012; Stüber et al, 2014).…”

Improving Imaging of the Brainstem and Cerebellum in Autistic Children: Transformation-Based High-Resolution Diffusion MRI (TiDi-Fused) in the Human Brainstem

“…The MPnRAGE pulse sequence is a novel imaging method that combines magnetization preparation using inversion recovery with a rapid 3D radial k-space readout (Kecskemeti et al, 2016 ). The MPnRAGE reconstruction enables retrospective head-motion correction (Kecskemeti et al, 2018 ), tissue-specific segmentation, and reliable quantitative T1 mapping (Kecskemeti et al, 2021 ).…”

“…To address the limitation of head motion in the TiDi-Fused processing, our T1w images were acquired with magnetization prepared rapid acquisition gradient echo (MPnRAGE; Kecskemeti et al, 2016 , 2018 ; Kecskemeti and Alexander, 2020a ). MPnRAGE retrospectively addresses head motion artifacts that are common in pediatric neuroimaging (Kecskemeti and Alexander, 2020b ), provides more reproducible cortical region definitions (Kecskemeti et al, 2021 ), and produces sharper delineations of gray/white matter boundaries than standard T1w images (Kecskemeti et al, 2018 ). The anatomical accuracy of MPnRAGE allows for high fidelity dMRI-to-T1w boundary-based registration.…”