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 + FslreorientFreesurfer: mri_convert -sphinx, mri_convert --in_orientationJip analysis toolkit: http://www.nmr.mgh.harvard.edu/~jbm/jip/jip-align/Web-based Reorient Tool: (https://neuroanatomy.github.io/reorient)
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 implemented in ANTs (ImageDenoise), SPM or Matlab package(https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging/mri-denoising
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 softwares such as fslmaths based on procedures described in Rilling et al., 2011, Front Evol Neurosci. 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	https://manpages.debian.org/testing/cmtk/cmtk-mrbias.1.en.html
3. Brain Extraction
Template-based	AntsBrainExtraction (ANTs), Atlasbrex (https://github.com/jlohmeier/atlasBREX)
Non Template-based	FSL-BET (can also be used with a template) bet_macaque.sh(https://github.com/neuroecology/MrCat/)
Deep Learning Model	U-NET (https://github.com/TingsterX/PRIME-DE/tree/master/BrainExtraction/)
Manual corrections	ITK-SNAP, BrainBox (https://brainbox.pasteur.fr/)
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	https://prime-re.github.io/templates_and_atlases.html
6. Ready-to-use Pipelines
Civet-Macaque	https://github.com/aces/CIVET_Full_Project
NHP-Freesurfer	https://github.com/VisionandCognition/NHP-Freesurfer/tree/public
PREEMACS	https://github.com/pGarciaS/PREEMACS/wiki
Macapype	https://github.com/Macatools/macapype
Precon_all	https://github.com/recoveringyank/precon_all
HCP-style NHP Pipeline	https://github.com/Washington-University/NHPPipelines&sa=D&ust=1588851113532000&usg=AFQjCNHdFJteT12kJx6tQuH8dxruBJUTsg