Image analysis methods and outputs
Lesions
Type (e.g. Gd-enhancing, T2-hyperintense, T1-hypointense)	T2 hyperintense lesions
Analysis method	Semi-automated edge detection contouring/thresholding technique
Analysis software	JIM version 6.0
Output measure (e.g. count or volume [ml])	mL
Tissue measures (e.g. MTR, DTI, T1-RT, T2-RT, T2*, T2’, 1H-MRS, perfusion, Na)
Type (e.g. whole brain, grey matter, white matter, spinal cord, normal-appearing grey matter or white matter)	Normal-appearing brain tissue, normal-appearing white matter, normal-appearing gray matter
Analysis method	SIENAX
Analysis software	FSL
Output measure	mL
Tissue measures (e.g. MTR, DTI, T1-RT, T2-RT, T2*, T2’, 1H-MRS, perfusion, Na)
Type (e.g. whole brain, grey matter, white matter, spinal cord, normal-appearing grey matter or white matter)	MTR of normal-appearing brain tissue, normal-appearing white matter, normal-appearing gray matter
Analysis method	Subtraction of images with and without MT pulse
Analysis software	In house
Output measure	Mean MTR value