Box 2 MRI protocol

1.

Sagittal 3D T1-weighted gradient-echo sequence (6–9 min).

E.g. MP-RAGE, SPGR, FFE

Correction for non-linear gradients (if applicable)

TE and TR according to local settings- giving good gray matter – white matter contrast

Slab thickness 180 mm, 180 partitions, 1.0 mm effective slice thickness

In-plane resolution 1.0 mm

2.

2D T2* gradient-echo sequence (3–5 min)

e.g. FLASH/FFE/SPGR, or (EPI-) SWI to obtain dark tissue background susceptible to T2* contrast –such as microbleedings.

TR ≥ 500 ms, TE ≥ 20 ms. Flip angle 20 degrees

Slice thickness 3 mm, no gap

Number of slices 48

In-plane resolution 0.5 – 1.0 mm

3.

2D T2-weighted FLAIR turbo/fast spin-echo (3–5 min)

TR 8,000 – 12,000 ms, TE 100–150 ms, TI 2,200 – 2,800 ms

Slice thickness 3 mm, no gap

Number of slices 48

In-plane resolution 0.5 – 1.0 mm

4.

2D T2-weighted turbo/fast spin-echo (3–5 min)

TR 2,000 - 4,000 ms, TE 80–120 ms

Slice thickness 3 mm, no gap

Number of slices 48

In-plane resolution 0.5 -1.0 mm

5.

2D Diffusion weighted imaging/EPI (30 sec-1 min)

Parallel Imaging on if possible (mandatory for 3 T)

TR 3,000-6,000 ms, TE 90–130 ms

Slice thickness < 5 mm, gap 10-30%

In plane resolution 2 mm b value (0/500/1000) or b value (0/900) or b value (0/1000) s/mm².

5b. Include online calculated ADC maps if possible.

6.

2D Diffusion tensor imaging (optional) (6–8 min)

Parallel Imaging on if possible (mandatory for 3 T)

TR 8,000-14,000 ms, TE 80–100 ms

Number of slices 56–70 slices

In-plane resolution 2.0 – 2.5 mm.

30–60 diffusion weighted directions with b = 1000 s/mm² , 5–6 scans with b = 0 s/mm²

Fat suppression ON

7.

2D Resting state fMRI (optional) (7–10 min)

3.0 Tesla scanner:

TR 1,800-2,200 ms, TE 30–40 ms, Flip Angle 80 degrees

Slice thickness 2.0 – 2.5 mm, gap 10%

Number of slices 38–54

In-plane resolution 2.0 – 2.3 mm

Number of volumes 200 (excluding run-in scans)

1.5 Tesla scanner:

TR 2,200-3,000 ms, TE 40–60 ms. Flip Angle 90 degrees

Slice thickness 2.5-3.0 mm, gap 10%

Number of slices 30–38

In-plane resolution 2.5 – 3.3 mm

Number of volumes 200 (excluding run-in scans)