Table 2.

Modifications of HCP-style preprocessing for NHP

Category of modification	Class	Modified or additional items in preprocessing pipeline
Measurement features	Static magnetic field (B0 )	Optimized distortion correction using B0 fieldmap and TOPUP, Note that this depends on both the resolution of imaging and the size of objects (e.g. brain) (see below).
	Radiofrequency field (B1 )	Optimized B1 biasfield correction in PreFreeSurferPipeline (BiasFieldSmoothingSigama) and FreeSurferPipeline (IntensityCor). The B1 bias field depends on the MR system (e.g. strength of magnetic field, configuration of transmitter and receiving coils) and objects (e.g. size and electromagnetic properties)
	Number of Wishart distributions	Computation of variance (VN) and estimation of dimensionality of fMRI data in ICA (icaDIM), which may depend on the interaction of the random noise of the measurement system with the voxel size, brain size, and processing steps
	Step length of diffusion tractography	25% of sampling resolution, depending on the spatial resolution of diffusion MRI
Neurobiological features	Field Of View (FOV)	Brain templates for T1w, T2w and subcortical ROIs (Atlas_ROIs), isometrically scaled for brain size
	Non-linear warp resolution	Configuration in FNIRT and TOPUP, isometrically scaled for brain size
	Scaling for FreeSurfer	Scaling and rescaling of brain image in FreeSurferPipeline, isometrically scaled for brain size
	Cortical thickness	Maximum cortical thickness in FreeSurferPipeline, adapted for histogram of cortical thickness in each species
	Cortical gyrification	Optimized max angle for search in surface registration (Marmoset = 50, Macaque = 68, Human = 68), which depends on the complexity of gyrification Template of surface registration in FreeSurfer (i.e. $GCAdir/?h.average.curvature.filled.buckner40.tif) and reference sulc for MSMSulc. Created for each species and used as a template of surface registration. See also effects of surface registration in Fig. 1S.
	Brain atlas and segmentation	Brain templates for structure MRI (T1w, T2w) and Atlas_ROIs. Species specific templates. Skull stripping of structure MRI of NHPs is also useful for initialization of registration Brain segmentation atlas for each species (i.e. Gaussian Classifier Atlas (GCA) at $GCAdir"/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz) White matter skeleton feeding in FreeSurferPipeline, adapted to thin white matter blades in NHPs. Needed for correct estimation of white surface.
	Registration of brain in fMRI	Use mcflirt_acc.sh for motion correction, use SE-EPI and T2w for initialization, use T1w-contrast FreeSurfer BBR for MION fMRI
	Artifact removal in fMRI	ICA+FIX training file, specific to species’s brain, measurement systems and contrasts (BOLD vs MION) Standard venous sinus maps in NIFTI volumes used for ICA+FIX
	Myelination	Population-based bias field correction of cortical myelin map, plus subject or scan-wise transmit field bias field correction is planned in future.

See also some of these features in the flow chart of the HCP-NHP pipelines in Fig. S1 in Autio et al. (2020b).