Published July 10, 2023 | Version 1.0.0
Software Open

R2*- and quantitative susceptibility mapping (QSM) post-processing pipelines for ex vivo rodent brains

Authors/Creators

  • 1. Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom
  • 2. SJTU-Ruijin-UIH Institute for Medical Imaging Technology, Shanghai, China
  • 3. 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
  • 4. 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 R2*- and QSM post-processing pipelines on data acquired at WIN's 7T Bruker facility. It should be compatible with any other data acquired on a similar Bruker scanner 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.

This pipeline is based on the code developed by Chaoyue Wang and Benjamin Tendler and published here: https://doi.org/10.1016/j.neuroimage.2020.117216. The scripts were either written or adapted by Cristiana Tisca.

The outputs of the pipeline include QSM and R2* maps.

 

Notes

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

Files

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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

  • Bautista, T. et al. (2021) 'Removal of Gibbs ringing artefacts for 3D acquisitions using subvoxel shifts', in Proc. Intl. Soc. Mag. Reson. Med., p. 3535.
  • Chakravarty, M. M. et al. (2013) 'Performing label-fusion-based segmentation using multiple automatically generated templates', Human Brain Mapping. doi: 10.1002/hbm.22092.
  • Eckstein, K. et al. (2018) 'Computationally Efficient Combination of Multi-channel Phase Data From Multi-echo Acquisitions (ASPIRE)', Magnetic Resonance in Medicine, 79(6), pp. 2996–3006. doi: 10.1002/mrm.26963.
  • Friedel, M. et al. (2014) 'Pydpiper: A flexible toolkit for constructing novel registration pipelines', Frontiers in Neuroinformatics. doi: 10.3389/fninf.2014.00067.
  • Gudbjartsson, H. and Patz, S. (1995) 'The rician distribution of noisy MRI data', Magnetic Resonance in Medicine, 34(6), pp. 910–914. doi: 10.1002/mrm.1910340618.
  • Jenkinson, M. (2003) 'Fast, automated, N-dimensional phase-unwrapping algorithm', Magnetic Resonance in Medicine, 49(1), pp. 193–197. doi: 10.1002/mrm.10354.
  • Kellner, E. et al. (2016) 'Gibbs-ringing artifact removal based on local subvoxel-shifts', Magnetic Resonance in Medicine. doi: 10.1002/mrm.26054.
  • Li, W. et al. (2015) 'A method for estimating and removing streaking artifacts in quantitative susceptibility mapping', NeuroImage. doi: 10.1016/j.neuroimage.2014.12.043.
  • Li, W., Wu, B. and Liu, C. (2011) 'Quantitative susceptibility mapping of human brain reflects spatial variation in tissue composition', NeuroImage. doi: 10.1016/j.neuroimage.2010.11.088.
  • Robinson, S. D. et al. (2017) 'Combining phase images from array coils using a short echo time reference scan (COMPOSER)', Magnetic Resonance in Medicine. doi: 10.1002/mrm.26093.
  • Schweser, F. et al. (2011) 'Quantitative imaging of intrinsic magnetic tissue properties using MRI signal phase: An approach to in vivo brain iron metabolism?', NeuroImage. doi: 10.1016/j.neuroimage.2010.10.070.
  • Tisca, C. et al. (2021) 'Vcan mutation induces sex-specific changes in white matter microstructure in mice', in Proc. Intl. Soc. Mag. Reson. Med. 29, p. 1226. Available at: https://index.mirasmart.com/ISMRM2021/PDFfiles/1226.html.
  • Tisca, C. et al. (2022) 'White matter microstructure changes in a Bcan knockout mouse model', in Proc. Intl. Soc. Mag. Reson. Med. 31.
  • Wang, C. et al. (2020) 'Methods for quantitative susceptibility and R2* mapping in whole post-mortem brains at 7T applied to amyotrophic lateral sclerosis', NeuroImage. Elsevier Inc., 222(May), p. 117216. doi: 10.1016/j.neuroimage.2020.117216.
  • Wang, C. et al. (2022) 'Phenotypic and genetic associations of quantitative magnetic susceptibility in UK Biobank brain imaging', Nature Neuroscience, 25(6), pp. 818–831. doi: 10.1038/s41593-022-01074-w.