NHP Issues

B. Why is NHP neuroimaging research and data so perplexing and challenging?

Even though the main gist of this guide concerns data processing, it is worthwhile to understand some of the pre-data processing issues related to NHP neuroimaging as these will give valuable insights into the source of the data processing issues that are typically encountered.

Prior to MR Acquisition

Several lengthy steps are necessary before being able to put a NHP individual in an MRI scanner. Here is a brief summary of those. An important implication is that typically NHP studies can recruit a lower number of subjects than in human studies. A corollary to this point is why it is so crucial that initiatives such as PRIME-DE exist to aggregate data from different centers to leverage the challenge of accessing more NHP data.

• Study preparation: Ethical approval (3R), “Recruitment” of non-human primates (find provider, transportation procedure, temporary house next to MR facility if the animal provider is far away, rearing and training for awake experiments etc.).

• Animal handling and preparation: Animal transportation to the MR room, anesthesia before and during the acquisition if needed, surgery for headpost fixation for awake task fMRI acquisition. A vet is also required to be present for the handling and the medical support during the acquisition. As a result, a huge amount of out-of-scanner preparation and time and cost is involved for each animal scan session.

• MR coil decision: Whether to build a home-made coil, buy a non-human primate coil already designed by a company or another lab, or to use clinical coils designed for humans (See Fig 1 for examples). This is in contrast with human MRI scans where a highly standardized birdcage coil is typically used and broadly available. Unfortunately, due to different head size and shape (one obvious difference between human and NHPs such as macaque or baboon is the elongated of ape’s mouth), those human coils are far from optimal from NHP studies and may even not fit one ape head even if the ape brain is much smaller than the human brain!

As a result, NHP MRI data often shows huge intensity inhomogeneity due to the inadequacy of the head size and the coil elements positioning (Figure 2). Surface coil may also be chosen for NHP MRIs, especially in the case of scanning using headpost or stereotaxic frames. The advantage of surface coils is the very strong receive signal in the vicinity of the coil but at the expense of a high intensity bias field. This strong intensity bias field, if not well taken care of (see part C 5.), will be problematic for processing stages such as skull stripping, registration and normalization. Also depending on the acquisition set-up, the head of the NHP individual may be far from the magnet isocenter, leading to image distortions due to the gradient non linearity in such areas.