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 ProtocolOpen Macaque Database (PRIME-DE)YA-HCP protocol
MRI scanner
Magnetic field strength (T)33 – 73
Gradient performance (mT/m)8040 - 80100
RF coil
Number of channels24*4 - 2432
Structural MRI
Spatial resolution (mm)0.50.3 – 0.50.7
T2wYesNo, YesYes
Functional MRI
Spatial resolution [mm]1.25*1.4 – 1.65 at 3T
1 - 1.2 at 7T
Repetition time (s)0.76*1.6 – 2.0 at 3T
1.0 at 7T
Echo-time (ms)3016 - 3033
Spin-echo fieldmapYes*NoYes
Gradient Echo FieldmapNoNo, YesNo
In-plane acceleration12 or NA1
Cross-plane acceleration (multiband factor)5*1, 2, NA8
Total scan time for resting-state fMRI (min/subject)102*13-476
(median = 41)
Total number of volumes for resting-state fMRI (volumes/subject)8192*500-13824
(median 1712)
Diffusion MRI
Spatial resolution [mm]0.9*1 - 1.4 at 3T
1.2 at 7T
Repetition time (s)3.46.3 – 11.0 at 3T
3.8 at 7T
Echo-time (ms)7383 -107 at 3T
54 at 7T
Number of b-shells3*1 - 33
b-value (mm2/s)1000-2000-3000*1000, 1600, 1250-2500
850-1650-2500 at 3T,
1500 at 7T
Number of diffusion gradient direction500*60, 80, 100, 120, 270270
Opposing-phase encoding acquisitionYesNo, YesYes
In-plane acceleration2NA1

*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.


NHP SpeciesConditionManagement ProtocolPositionMRI ProtocolReferences

Macaque Anesthesia Protocol (793 downloads )


NHP-HCP_MacaqueSedatedBOLD_v1.0.pdf (763 downloads )

NHP-HCP_MacaqueSedatedBOLD_v1.0-1.exar1 (463 downloads )