Table 3.
Comparison of protocols used by 3 research groups for ultrahigh-resolution imaging of formalin-fixed ex vivo human brain specimens.
| Feature | Paxinos et al. (2023) | Naidich et al. (2009) | Current study |
|---|---|---|---|
| Specimen preparation | Perfused with saline ex vivo, immersion fixed in 10% formalin, soaked in neural phosphate buffered saline doped with 2.5 mM gadoteridol for 3 weeks | 10 formalin-fixed cadaver tissue samples fixed in 15% formalin for 2 weeks, suspended in phosphate buffer, and then imaged |
PMI 168 h, 4% formalin fixation for 6 months, followed by rehydration with normal saline for 7 days prior to imaging |
| Field strength | 7T | 9.4T | 7T |
| Magnet type | Agilent Direct Drive MRI system (Agilent Technologies, Santa Clara, CA) | Bruker Magnex superconducting magnet with 89-mm vertical bore (Bruker Analytik, Rheinstetten, Germany) |
Bruker Biospec 70/30, with 30-cm bore size (Bruker Corporation, Billerica, MA) |
| RF coil | 65 × 100-mm quadrature RF coil | 30-mm bird cage coil | 70-mm volume coil |
| Pulse sequence | Simple diffusion-weighted spin echo pulse sequence TR/TE = 100 ms/33.6 ms, BW = 278 Hz/pixel | Pulsed gradient spin echo sequence: TR = 12,000 ms, TE = 25.7 ms |
Custom sequence for DTI and FLASH for anatomical imaging, TR/TE = 3,500/15 ms for sagittal, 1,500/9 ms for coronal and axial |
| b-value | 4,000 s/mm2 | 1,600 s/mm2 | 3,105 s/mm2 |
| Gradient settings | δ = 4.7 ms, Δ = 26 ms | Not specified | δ = 7 ms, Δ = 14 ms |
| Diffusion directions | 120 directions | 6 directions | 60 directions |
| Voxel size | 200 μm isotropic | 1-mm slice thickness, data matrix: 128 × 128 |
In-plane resolution 0.55 mm, slice thickness 0.5 mm |
| Scan duration | 208 h | 24 h for 24 slices | 48 h and 48 min |
| Data analysis software | Custom postprocessing pipelines | DtiStudio v2.4 | DSI Studio, DIPY |
| Tractography method | Not specified | FACT algorithm | Deterministic algorithm in DSI Studio |
| Additional imaging | High-resolution GRE images | Color maps and eigenvector maps for visualization | High-resolution anatomical imaging with FLASH sequence |
Δ, separation; δ, width; BW, bandwidth; DIPY, diffusion imaging in phyton documentation; DSI, diffusion spectrum imaging; DTI, diffusion tensor imaging; FACT, fiber assignment by continuous tracking; FLASH, fast low-angle shot; GRE, gradient echo; MRI, magnetic resonance imaging; PMI, postmortem interval; TE, time to echo; TR, repetition time.