MRI data analysis: muscle quantitative MRI

A single observer (E.V.) with a 5-year training expertise and blinded to study groups outlined for each participant regions of interest (ROIs) on the 1st echo of the ME-SE sequence at mid-thigh (12 muscles) and mid-calf level (6 muscles) using ITK-SNAP software [21]. ROIs were then transferred to the 1st echo of the ME-GRE acquisition and manually adjusted to ensure proper alignment. All ROIs were verified by two expert neuroradiologists (A.P. and M.P.) with more than 5-year expertise in neuromuscular imaging.

The ME-SE sequence was processed using a bi-component extended phase graph algorithm, implemented in Python, for quantification of water T2 (wT2) [22, 23], using an open-source toolbox [24]. The Fatty Riot algorithm was used offline for the calculation of fat/water images from the ME-GRE acquisition [25, 26] and then FF maps were obtained (FF = F/F + W*100%) from each ROI. Average values of FF and wT2 were calculated for the global ROI and for each muscle at thigh and calf level.

Figure 1 shows the muscles of the lower limbs which have been assessed. The tibialis posterior (TP) was not evaluated according to the poor quality of visualization at calf MRI.

Thigh and calf single muscle ROIs and compartments. Thigh (A) and calf (B) single muscle ROI of a healthy control superimposed on multi-echo spin-echo (ME-SE) sequence (1st echo) to extract water T2 values and on multi-echo gradient-echo (ME-GRE) sequence (1st echo) to obtain fat fraction maps. Thigh and calf compartments are reported on the right