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. 2024 Jul 31;14(7):e082161. doi: 10.1136/bmjopen-2023-082161

Table 3. Overview of MRI data.

MRI sequences Acquisition parameters Rationale and outcome indices
Magnetisation-prepared rapid gradient-echo (MP-RAGE) 1 mm3 resolution, FOV: 256×256, TR=2300 ms, TE=2 ms, TI=857 ms, flip angle: 9; Duration~7 min 3-dimensional (3D) T1-weighted anatomical image

  • For the segmentation of regions of interests in the basal ganglia, sensori-motor cortices and cerebellum

  • As reference map for all microstructural outcome maps
Multi-shell High Angular Resolution Diffusion Imaging (msHARDI)33 2 mm3 resolution; FOV: 220×200; matrix size: 110×110 x 66; TE/TR=59/3000 ms; δ/Δ: 7/24 ms; b-values=0 (14 volumes), 500 (30 directions), 1200 (30 directions), 2400 (60 directions), 4000 (60 directions) and 6000 (60 directions) s/mm2; Duration ~20 min Multishell diffusion weighted imaging data

  • For multitissue constrained spherical deconvolution-based54 tractography to reconstruct white matter pathways of interest (corpus callosum, cortico-spinal tract, connections between caudate and prefrontal cortex, connections between putamen and supplementary motor area/motor cortex)

  • For modelling of white matter tissue properties with the Composite Hindered And Restricted Model of Diffusion 41 yielding the restricted signal fraction (FR) as an estimate of axon density and the Neurite Orientation Dispersion and Density Imaging42 yielding the isotropic signal fraction as an estimate of free water and the orientation dispersion index as an estimate of axon orientation and dispersion.

  • for modelling of grey matter tissue properties with the Soma And Neurite Density Imaging model35 yielding estimates of soma density (soma signal fraction) and size.
Quantitative magnetisation transfer (qMT)55 56 1.72 mm3 resolution; FOV 220×220×179 mm; matrix size 128×128 x 104; turbo flash sequence, turbo factor 4, non-selective excitation MT pulse duration: 15.3 ms, 11 MT-weighted volumes and 1 vol without MT-weighting, 11 Frequency offsets (Hz) and 11 flip angles (degrees): 47 180 (628°); 56 360 (332°); 12060, (628°); 1000 (332°);1000 (333°); 2750 (628°); 2770 (628°); 2790 (628°); 2890 (628°); 1000 (628°); 1000 (628°); Duration ~25 min qMT data to model the macromolecular proton fraction as an estimate of white matter myelin content36.
Multicomponent-driven equilibrium single pulse observation of T1 and T2 (mcDESPOT)37 1.72 mm3 resolution; FOV 220×220×179 mm; matrix size 128×128×104;T1-weighted 3D spoiled gradient-recalled echo sequence (SPGR) with TR=4 ms; TE=1.9 ms; 8 flip angles (3°, 4°, 5°, 6°, 7°, 9°, 13° and 18°); Inversion recovery-prepped spoiled gradient-recalled echo sequence with TR=4 ms; TE=1.9 ms; flip angle 5°; steady-state free precession with TR=4.54 ms, TE=2.27 ms, 8 flip angles (10°, 13.33°, 16.67°, 20°, 23.33°, 30°, 43.33° and 60°), duration ~14 min mcDespot data to model

  • The myelin water fraction as an estimate of white matter myelin

  • To estimate T1 and B1 fields for qMT analyses

FOV, field of view; mcDESPOT, Multicomponent Driven Equilibrium Single Pulse Observation of T1 and T2; MT, magnetisation transfer; TE, echo time; TI, inversion time; TR, repetition time