PyDesigner
PyDesigner is a piece of software developed in-house for the purposes of artifact correction and tensor calculation. This process takes raw data (either nifti or dicom format) and corrects that data of known artifacts and then outputs parametric maps which are used for downstream analysis.
For an automated script to run PyDesigner on your BIDS formatted data, see: https://github.com/ryn-thorn/Image_Analysis_Scripts/blob/main/pyd_preproc.sh
You can find more information about PyDesigner, including installation procedures and user guidance here: PyDesigner v1.0: A Pythonic Implementation of the DESIGNER Pipeline for Diffusion Magnetic Resonance Imaging on JoVE (the Journal of Visualized Experiments)
In short, PyDesigner can be installed with the command:
pip install PyDesigner-DWIAnd called with the following command:
pydesigner -o [output path] -s [input path].niiLast updated