MRI Acquisition

MR images were acquired with a Siemens 3T MAGNETOM Skyra scanner using an 18-channel surface coil for the thigh muscle MRI, while for MRI of the SC, a 20-channel head/neck coil was combined with the 12-channel spine array integrated into the patient table.

The muscle MRI protocol was centered on the thighs, with simultaneous acquisition of both sides (total scanning time of approximately 15 min). The MRI protocol included a 3D six-point multi-echo gradient echo (GRE) sequence with interleaved echo sampling (matrix size = 432 × 396 × 52, TR = 35 ms, 6 echo times, TE = 1.7–9.2 ms, ΔTE = 1.5 ms, resolution = 1.0 × 1.0 × 5.0 mm³) and a turbo spin echo T2 multi-echo sequence (TE = 10.9 ms, TR = 4100.0 ms, resolution = 1.2 × 1.2 × 10.0 mm³, 17 echo times).

The SC MRI protocol adopted for this study is derived from the consensus acquisition protocol produced by a consortium of SC researchers [(31); Cohen-Adad et al., Submitted, https://spine-generic.readthedocs.io/en/latest/]. The whole protocol included T1-weighted (sagittal 3D MPRAGE, field of view = 320 × 260 × 192 mm³, resolution = 1.0 × 1.0 × 1.0 mm³, TI/TR/TE = 1,000/2,000/3.72 ms) and T2-weighted 3D morphological sequences (sagittal 3D SPACE, field of view = 256 × 256 × 52 mm³, resolution = 0.8 × 0.8 × 0.8 mm³, TR/TE = 1,500/120 ms), with the T1w volume providing full coverage of the brain and the T2w volume centered on the cervical SC at the level of the C3–C4 vertebral disc. These were followed by a DWI acquisition (axial 2D SE-EPI, field of view = 86 × 33 × 75 mm³, resolution = 0.9 × 0.9 × 5.0 mm³, TR/TE = 620/60 ms, b = 800 s/mm², 30 directions) using the Siemens ZOOMit technology for reduced FOV (32) and cardiac gating a set of three 3D gradient echo sequences for MT imaging [axial, field of view = 230 × 230 × 110 mm³, resolution = 0.9 × 0.9 × 5.0 mm³, TR/TE = 35(15)/3.13 ms], and a 2D T2^*-weighted (axial 2D MEDIC, field of view = 224 × 224 × 75 mm³, resolution = 0.5 × 0.5 × 5.0 mm³, TR/TE = 600/14 ms) scan, all centered at the level of C3–C4 vertebral disc. The total acquisition time for the cervical SC MRI was approximately 30 min, depending on heart rate.