Structural processing

D. Main steps in NHP structural data processing and available PRIME-RE tools

Here we provide an overview of the main steps involved, and the tools available in PRIME-RE or in existing neuroimaging software packages, for the processing of NHP structural images with the goal of achieving an extracted brain mask and the segmentation masks (WM,GM and CSF). We also provide a list of existing pipelines for macaque anatomical processing for reference.

Processing Step	Available Tools
1. Data Preparation
Reorientation	FSL: fslreorient2std, fslswapdim + fslreorient Freesurfer: mri_convert -sphinx, mri_convert --in_orientation Jip analysis toolkit Web-based Reorient Tool
Deoblique	AFNI: 3drefit -deoblique (for changing header information)
Cropping	FSL: fslroi, FSLeyes AFNI: @clip_volume FreeSurfer: mri_convert --slice-crop
Denoising	Adaptive non-local means filter denoising in ANTs (ImageDenoise), SPM or Matlab package
Averaging multiple images	Linear Registration tools: FSL-FLIRT, AFNI-3dVolReg, 3dAllineate, SPM Register, etc. Image averaging: fslmaths, SPM Imcalc, etc.
2. Bias-Correction
T1xT2 bias field correction (HCP Method)	Can be implemented using standard image calculation software such as fslmaths based on procedures described in Rilling et al. (2011) A module for this bias-correction is also available in Macapype (correct_bias.py).
N3, N4BiasFieldCorrection	Available in ANTs, MINC, Freesurfer packages. One could also consider N3biascorrection which works better in some cases.
FSL-Fast	FSL
CMTK-mrbias	Find it here
3. Brain Extraction
Template-based	AntsBrainExtraction (ANTs), Atlasbrex
Non Template-based	FSL-BET (can also be used with a template), bet_macaque.sh
Deep Learning Model	U-NET
Manual corrections	ITK-SNAP, Slicer, BrainBox
4. Brain Segmentation
Template-based	AntsAtroposN4 script, Atropos (ANTs), SPM Segment
Non Template-based	FSL-Fast (can be used with templates)
Manual segmentations/corrections	ITK-SNAP, BrainBox
5. Templates and Atlases	See PRIME-RE
6. Ready-to-use Pipelines
Civet-Macaque	Find it here
NHP-Freesurfer	Find it here
PREEMACS	Find it here
Macapype	Find it here
Precon_all	Find it here
HCP-style NHP Pipeline	Find it here