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This repository includes scripts for preprocessing of task-free single-echo functional MRI scans. The submission scripts are designed for use with the HPHI high performance computing hub at the University of Cambridge. The preprocessing order is as follows:

• co-registration of functional and structural images and creation of warp files for normalising to standard (MNI) space
• initial operations to prepare images for analysis
• removal of movement artefact using wavelet despiking
• regression of variours parameters
• application of warping to normalise to standard (MNI) images

From there the analysis can continue to generate association matrices for using in graph analysis:

• parcellation and extraction of timeseries
• wavelet cross-correlation to generate association matrices

Alternatively, it can be used to prepare images for ICA analysis (eg using FSL's melodic tool):

• ensuring scan lengths are identical

Publications

Cope et al, Tau burden and the functional connectome in Alzheimer's disease and progressive supranuclear palsy, Brain 2018. 141:550-67 Rittman et al, Regional expression of the MAPT gene is associated with loss of hubs in brain networks and cognitive impairment in Parkinson's disease and Progressive Supranuclear Palsy. Neurobiology of Aging 2016. 48: 153-60