Published July 10, 2023 | Version 1.0.0
Software Open

A diffusion-weighted MRI post-processing pipeline for ex vivo rodent brains to extract DTI, DKI and NODDI metrics

Authors/Creators

  • 1. Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom
  • 2. Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom and Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
  • 3. Senior Author, Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom

Description

This repository contains all scripts to run the ex vivo diffusion-weighted MRI (dMRI) post-processing pipeline on data acquired at WIN's 7T Bruker facility. It should be compatible with any other data acquired on a similar Bruker scanner and using an equivalent protocol.

This resource contains anonymised file-paths which will need to be edited to enable running on a cluster facility. The commands for submitting jobs to the cluster also need to be edited.

The outputs of the pipeline include the standard DTI (FA, MD, V1) and DKI (FA, AK, RK, K1) outputs from FSL's dtifit and the standard NODDI outputs (OD, ICVF, ISOVF) from cuDIMOT.

Notes

Additional funding sources: Wellcome Trust Senior Research Fellowship (Renewal), Prof Karla Miller, 224573/Z/21/Z

Files

bruker-7-t-dmri-pipeline-ex-vivo-open-source.zip

Files (3.6 MB)

Additional details

Funding

UK Research and Innovation
EPSRC and MRC Centre for Doctoral Training in Biomedical Imaging EP/L016052/1
Wellcome Trust
Linking MRI and microscopy for multi-scale neuroscience: Mechanisms, diagnostics and anatomy 202788
Wellcome Trust
Integrative imaging of brain structure and function in populations and individuals 215573
Wellcome Trust
Wellcome Centre for Integrative Neuroimaging 203139

References

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