MRtrix3 is a neuroimaging program that can be used to performed diffusion MRI analyses. Official mrtrix3 documentation can be found here. It is advised you follow the official documentation and pipelines as it is updated frequently by the developers. The following pages are written as rough guide/documentation for some of the pipelines that are currently being used specifically for certain sequences obtained in Frontier (these pipelines are not suitable for ALL scans). MRtrix3 also has a community forum in which you can find solutions to common problems, or where you can ask your own questions.
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For official pipelines, refer to the tutorials and workflows on the mrtrix3 docs e.g. for quantitative analysis, or FBA. To view a custom pipeline made specifically for certain Frontier scans (FTD0001-FTD12##):
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For custom pipelines created for certain Frontier sequences obtained in NeuRA (FTD0001-FTD12##), click /wiki/spaces/FN/pages/2014773650.
Most sequences obtained at the BMC should contain reversed phase-encoded image data, which allows a simpler pre-processing pipeline (Basic DWI preprocessing) using dwipreproc.