Table 11 Research MRI protocol: brain and cervical spine

3D T1W

Brain

(~ 6 min)

• Sagittal acquisition

• 1x1x1mm or smaller

Volumetric analysis, registration

3D FLAIR

Brain

(~ 6 min)

• Sagittal acquisition

• 1x1x1mm or smaller

• Match geometry to 3D T1W

Lesion identification and quantification.

Use with T2*/QSM for central vein, iron rim detection

T2*/QSM

Brain

(~ 6 min)

• 3D multi echo gradient echo

• Axial acquisition

• In plane resolution 0.6 × 0.6 mm

• Slice thickness 1 mm (can acquire at 2 mm and reconstruct to 1 mm if available)

• TE 5, 13, 20, 27, 34, 41 ms

Identification of iron rims, central veins in lesions, and QSM may help to detect microstructural changes relevant to progression

MWI (optional)

Brain (~ 6 min)

• 3D GRASE

• Acquired voxel 1x2x5mm, reconstructed voxel 1x1x2.5 mm

• 48 echoes with TE 8 ms

To detect changes in myelin in lesions and NAWM

DTI

Brain (~ 4 min)

• Isotropic voxels 1.7 × 1.7 × 1.7 mm

• 30 directions TR/TE = 4700/64 ms

• b = 1000s/mm²

To use with T2* to assess structural connectivity, ROI definition

MTsat

Brain

(~ 9 min)

• MTon and MToff (TR 25 ms, flip angle 5 degrees), T1W (TR 11 ms, flip angle 15 degrees)

• TE 3 ms

• Off-resonance Gaussian MT pulse

• Sagittal 1.5 × 1.5 × 1.5 mm

Detect changes in myelin in lesions and NAWM

PSIR or STIR

Cervical SC (~ 5 min)

• Sagittal 0.7 × 0.7x3mm (or better)

Lesion identification

T2W

Cervical SC

(~ 5 min)

• 3D TSE

• Sagittal 0.8 × 0.8 × 0.8 mm

Quantifying SC CSA, registration to template, nerve root identification

MTsat

Cervical SC

(~ 7–15 min)

• 3D GRE

• Axial 0.9 × 0.9x5mm

• TE ~ 2 ms

• MTon and MToff: TR ~ 50 ms, Flip Angle 9 degrees, T1W: TR = 15 ms, Flip Angle 15 degrees

Quantifying myelin in SC

Multi-slice multi-echo gradient echo

Cervical SC (~ 4 min)

• Resolution should be 0.5 mm in plane

• Slice thickness of 5 mm

Lesion identification and grey matter segmentation in SC