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Abstract

Neuroscience

PyDesigner v1.0: A Pythonic Implementation of the DESIGNER Pipeline for Diffusion Magnetic Resonance Imaging

Published: May 17th, 2024

DOI:

10.3791/66397

1Department of Neuroscience, Medical University of South Carolina, 2Department of Neurology, Medical University of South Carolina, 3Center for Biomedical Imaging, Medical University of South Carolina, 4Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, 5Department of Radiology and Radiological Science, Medical University of South Carolina

* These authors contributed equally

Abstract

PyDesigner is a Python-based software package based on the original Diffusion parameter EStImation with Gibbs and NoisE Removal (DESIGNER) pipeline (Dv1) for dMRI preprocessing and tensor estimation. This software is openly provided for non-commercial research and may not be used for clinical care. PyDesigner combines tools from FSL and MRtrix3 to perform denoising, Gibbs ringing correction, eddy current motion correction, brain masking, image smoothing, and Rician bias correction to optimize the estimation of multiple diffusion measures. It can be used across platforms on Windows, Mac, and Linux to accurately derive commonly used metrics from DKI, DTI, WMTI, FBI, and FBWM datasets as well as tractography ODFs and .fib files. It is also file-format agnostic, accepting inputs in the form of .nii, .nii.gz, .mif, and dicom format. User-friendly and easy to install, this software also outputs quality control metrics illustrating signal-to-noise ratio graphs, outlier voxels, and head motion to evaluate data integrity. Additionally, this dMRI processing pipeline supports multiple echo-time dataset processing and features pipeline customization, allowing the user to specify which processes are employed and which outputs are produced to meet a variety of user needs.

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