This page describes protocols of MRI scanning and managements of animals during scans, used in NHP_NNP. The MRI protocol follows the HCP-like approach (see Autio et al., 2020), thus named as HCP-NHP protocols, and intends to collect high-quality, high-resolution MRI images to be analyzed for surface-based approach in macaque (Van Essen et al., 2012). HCP-NHP protocols are performed using a 3T MRI scanner (Siemens MAGNETOME Prisma) and a macaque head 24-ch radio-frequency (RF) receiving coil (Rogue Research Inc./Takashima Seisakusho Co., LTD).
HCP-NHP MRI Protocol is summarized below in comparison with open database for macaque (PRIME-DE) and Young Adult Human Connectome Project (YA-HCP). HCP-NHP MRI Protocol is downloadable by PDF and EXAR1 formats.
Summary of HCP-NHP MRI Protocols Compared with Other Projects
| HCP-NHP Macaque Protocol | Open Macaque Database (PRIME-DE) | YA-HCP protocol |
|
| MRI scanner | |||
| Magnetic field strength (T) | 3 | 3 – 7 | 3 |
| Gradient performance (mT/m) | 80 | 40 - 80 | 100 |
| RF coil | |||
| Number of channels | 24* | 4 - 24 | 32 |
| Structural MRI | |||
| Spatial resolution (mm) | 0.5 | 0.3 – 0.5 | 0.7 |
| T1w | Yes | Yes | Yes |
| T2w | Yes | No, Yes | Yes |
| Functional MRI | |||
| Spatial resolution [mm] | 1.25* | 1.4 – 1.65 at 3T 1 - 1.2 at 7T | 2 |
| Repetition time (s) | 0.76* | 1.6 – 2.0 at 3T 1.0 at 7T | 0.72 |
| Echo-time (ms) | 30 | 16 - 30 | 33 |
| Spin-echo fieldmap | Yes* | No | Yes |
| Gradient Echo Fieldmap | No | No, Yes | No |
| In-plane acceleration | 1 | 2 or NA | 1 |
| Cross-plane acceleration (multiband factor) | 5* | 1, 2, NA | 8 |
| Total scan time for resting-state fMRI (min/subject) | 102* | 13-476 (median = 41) | 58 |
| Total number of volumes for resting-state fMRI (volumes/subject) | 8192* | 500-13824 (median 1712) | 4800 |
| Diffusion MRI | |||
| Spatial resolution [mm] | 0.9* | 1 - 1.4 at 3T 1.2 at 7T | 1.25 |
| Repetition time (s) | 3.4 | 6.3 – 11.0 at 3T 3.8 at 7T | 5.5 |
| Echo-time (ms) | 73 | 83 -107 at 3T 54 at 7T | 90 |
| Number of b-shells | 3* | 1 - 3 | 3 |
| b-value (mm2/s) | 1000-2000-3000* | 1000, 1600, 1250-2500 850-1650-2500 at 3T, 1500 at 7T | 1000-2000-3000 |
| Number of diffusion gradient direction | 500* | 60, 80, 100, 120, 270 | 270 |
| Opposing-phase encoding acquisition | Yes | No, Yes | Yes |
| In-plane acceleration | 2 | NA | 1 |
*Imaging parameters that are important in the current HCP-NHP protocol and were never or not often applied in PRIME-DE database. For reference, those of the young adult HCP protocol is shown in the right column. NA: not available.
HCP-NHP Animal Management Protocol
This section describes the methods and managements of animals before and during MRI scanning, including anesthesia and preparation. For maintenance of anesthesia, two types of anesthetics, isoflurane and dexmedetmidine are used to achieve a stable anesthetic condition during long scanning of functional MRI. The protocol is downloadable in PDF format below.
Downloads
| NHP Species | Condition | Management Protocol | Position | MRI Protocol | References |
| Macaque | Anesthesia | Supine | [3] | ||
| Awake | TBA | TBA | TBA | TBA | |
| Marmoset | Anesthesia | TBA | TBA | TBA | TBA |
| Awake |