Author: Lenore Tahara-Eckl Email: [email protected]
These scripts have been created for analysing and visualising the neuroimaging (e.g. diffusion MRI (dMRI), functional MRI (fMRI)) and neuropsychological data from the Dementia Prevention Research Clinic (DPRC), at the University of Auckland, New Zealand.
Please read manuals (.docx files, located in the 'manuals' folder) to learn more about the scripts generated for the DPRC dMRI data analysis. Specific diffusion analysis include preprocessing/cleaning dMRI data, constrained spherical deconvolution (CSD), fixel-based analysis (FBA), and creating a structural diffusion and functional connectome. Scripts are written mainly in Matlab R2020b, and in R (version 4.0.3) and Python (version 3.8.3), functioning with both code and a wrapper which primarily calls commands from MRtrix3 (Tournier et al., 2019; https://www.mrtrix.org/), and also from FMRIB Software Library (FSL) (Jenkinson, Beckmann, Behrens, Woolrich, & Smith, 2012; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation). Other softwares / GitHub repositories which are utilised are Advanced Normalisation Tools (ANTs) (Avants et al., 2011; http://stnava.github.io/ANTs/), FreeSurfer (https://surfer.nmr.mgh.harvard.edu/), fmriprep (Esteban et al., 2019; https://fmriprep.org/en/stable/; version 20.2.1), and Denoiser (https://github.com/arielletambini/denoiser) (these must all be downloaded / installed for use).
Please visit websites of the above software programmes and cite the original authors of the programme, if you wish to use this.