Table 3.

Image processing pipelines and measurement outcomes

Sequence type	Processing pipelines	Measurement outcome
3D-T1-weighted	Freesurfer V.6.0	Whole brain and regional volumes cortical thickness
FLAIR	Cerebra-LET (CIPAC)	White matter hyperintensity volumes
rs-fMRI	FSL	Default mode network connectivity
DWI	FSL, ExploreDTI	FA, MD, RD, PSMD, structural connectivity
qT1	CIPAC custom pipeline	Mean regional T1 values, VBM
qT2	StimFit27	Mean regional T2 values, VBM
QSM	CIPAC custom pipeline	Mean regional susceptibility values, mean regional T2* values, cerebral microbleed detection
pcASL	GE scanner generated CBF maps; BASIL (FSL)	Mean regional CBF values

T1, spin–lattice relaxation time constant; T2, spin–spin relaxation time constant.

BASIL, Bayesian inference for arterial spin labeling; CBL, cerebral blood flow (mL/min/100 g tissue); Cerebra-LET, Cerebra Lesion Extraction Tool; CIPAC, calgary image processing and analysis centre; DWI, diffusion-weighted imaging; FA, fractional anisotropy; MD, mean diffusivity; pcASL, pseudo-continuous arterial spin labelling; PSMD, peak skeletonised mean diffusivity; QSM, quantitative susceptibility mapping; RD, radial diffusivity; rs-fMRI, resting state functional magnetic resonance imaging.