Functional processing

E. Main steps in NHP functional data processing and available PRIME-RE tools

[ To be updated! ]
A substantial part of dealing with NHP fMRI data is very similar to dealing with human fMRI data. Once your data is in good shape, the statistical analysis of time-courses is nothing special. However, getting your data in good shape can be challenging, especially when your working with awake animals performing tasks.

Realignment and motion correction correction is crucial. Awake animals will always move a little, and while the movements themselves might be easily correct (especially when the animals are head-fixed), the distortions in the homogeneity of the magnetic field caused by body movements are more difficult to get rid of. The best advise we can give is try to avoid or reduce them as much as possible!

There are two main strategies:

• Anesthetize the animal (obviously this is not possible if the animals needs to perform a task)
• Train the animals extensively and use good fixation methods (several invasive and non-nonvasive head-holding systems have been developed)

If you still end up with significant motion issues a common approach is to perform:

• Non-rigid slice-by-slice realignment
• Volume-based motion correction

Useful reference: Farivar and VanDuffel (2014): Functional MRI of Awake Behaving Macaques Using Standard Equipment, Advanced Brain Neuroimaging Topics in Health and Disease - Methods and Applications, Chapter 6.

Check the PRIME-RE website for the most recent list of resources for NHP fMRI

Ready-to-use Pipelines	Link to the Resources
afni_proc.py	https://prime-re.github.io/pipelines_fmri.html#afni_procpy
MR Comparative Anatomy Toolbox (MrCat)	https://prime-re.github.io/pipelines_fmri.html#mr-comparative-anatomy-toolbox-mrcat
NeuroElf	https://prime-re.github.io/pipelines_fmri.html#neuroelf
NHP-BIDS	https://prime-re.github.io/pipelines_fmri.html#nhp-bids
NHP-pycortex	https://prime-re.github.io/pipelines_fmri.html#nhp-pycortex
Pypreclin	https://prime-re.github.io/pipelines_fmri.html#pypreclin