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Box 2 MRI protocol

From: The Dutch Parelsnoer Institute - Neurodegenerative diseases; methods, design and baseline results

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)