🧠
BRIDGE Lab Documentation
  • BRIDGE Lab Documentation
  • 📘General
    • About Us
    • Onboarding
      • First Steps
      • Research Specialist Training
      • Project Coordinator Training
    • Misc
      • How to do misc things
      • Burning Scans to a Disc
      • Setting Up Meetings in the Conference Room
      • Printing
    • Imaging Glossary
  • 🖇️Admin
    • Ourday
    • Training
    • Regulatory
    • Social Media
    • REDCap
      • Archiving REDCap Projects
  • 🖥️Tech
    • Setting Up Meetings in the Conference Room
    • Effective Troubleshooting
    • Remote Work Resources
    • Arthur
    • Servers
      • Connecting to an External Server
    • Bash 101
      • What is Bash?
      • Bash Examples
      • How to add elements to your bash profile
    • git and Github
  • 🩻Image Acquisition
    • ViSTa
  • 🗃️Data Organization
    • BIDs Data Formatting
    • MRI Data Organization
  • 🖼️Image Analysis
    • Image QC
      • Raw Data QC
        • Diffusion QC
        • T1/T2 QC
        • ViSTa QC
        • Spectroscopy QC
      • PyDesigner QC
    • Project Lifecycle
    • General Concepts
    • Raw Data
    • Preprocessing
      • Denoising UNI MP2RAGE Images
      • PyDesigner
      • ViSTa
    • Native Space Analysis
      • TractSeg
        • TractSeg + Within-Subject Registration
      • Segmentation
        • LST
        • Freesurfer
        • NOMIS
    • Registration
      • DTI-TK
      • TBSS
      • Coordinate Systems
    • Other Pipelines
    • Archiving
  • 📊Data Viz and Stats
    • Plotting in R
  • 📚Imaging Library
Powered by GitBook
On this page
  1. Image Analysis
  2. Preprocessing

PyDesigner

Last updated 1 year ago

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.

You can find more information about PyDesigner, including installation procedures and user guidance here:

See also:

In short, PyDesigner can be installed with the command:

pip install PyDesigner-DWI

And called with the following command:

pydesigner -o [output path] -s [input path].nii
🖼️
PyDesigner v1.0: A Pythonic Implementation of the DESIGNER Pipeline for Diffusion Magnetic Resonance Imaging on JoVE (the Journal of Visualized Experiments)
GitHub - muscbridge/PyDesigner: A hands-free DTI, DKI, FBI and FBWM preprocessing pipeline. Information on algorithms and preprocessing steps are available at https://www.biorxiv.org/content/10.1101/2021.10.20.465189v1 A video tutorial on PyDesigner and its usage is now available at https://www.youtube.com/watch?v=mChQFuQqX3kGitHub
Logo