AUTHOR=Valcourt Caron Alex , Shmuel Amir , Hao Ziqi , Descoteaux Maxime 

TITLE=versaFlow: a versatile pipeline for resolution adapted diffusion MRI processing and its application to studying the variability of the PRIME-DE database

JOURNAL=Frontiers in Neuroinformatics

VOLUME=Volume 17 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2023.1191200

DOI=10.3389/fninf.2023.1191200

ISSN=1662-5196

ABSTRACT=The lack of "gold standards" in Diffusion Weighted Imaging (DWI) makes validation cumbersome. To tackle this task, studies use translational analysis where results in humans are benchmarked against findings in other species. Non-Human Primates (NHP) are particularly interesting for this, their cytoarchitecture being closely related to humans. However, tools used for processing and analysis must be adapted and finely tuned to work well on NHP images. Here, we propose versaFlow, a pipeline implemented in Nextflow, designed for robustness and scalability, in modules to allow for maintainability and customization, tailored to in-vivo NHP DWI at any spatial resolution. Processes and workflows are implemented upon cutting edge and state-ofthe-art Magnetic Resonance Imaging (MRI) processing technologies and diffusion modeling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained Spherical Deconvolution (CSD) and DIstribution of Anisotropic MicrOstructural eNvironments in Diffusion-compartment imaging (DIAMOND). Using versaFlow, we provide an in-depth study of the variability of diffusion metrics computed on 32 subjects from 3 sites of the Primate Data Exchange (PRIME-DE), which contains anatomical T1-weighted (T1w) and T2-weighted (T2w) images, functional MRI (fMRI) and DWI of NHP brains. Together, they offer images acquired over a range of resolutions, using single and multi-shell gradient samplings, on multiple scanner vendors. We perform a reproducibility study of the processing of versaFlow using the Aix-Marseilles site, to ensure our implementation has minimal impact on variability observed in further analyses. We report very high reproducibility from a majority of metrics; only gamma distribution parameters of DIAMOND display less reproducible behaviors, due to the absence of a mechanism to enforce a random number seed in the software we used. This should be taken into consideration when future applications are performed. We show that the PRIME-DE diffusion data exhibits a great level of variability, similar or greater than results obtained in human studies. Its usage should be done carefully to prevent instilling uncertainty in statistical analyses. This hints at a need for sufficient harmonization in acquisition protocols and for the development of robust algorithms able to correct for the variability induced in imaging from the difference in vendor and from models produced by the same vendor.