Web Reference: MRtrix Tutorial #3: Looking at the Data Overview MRtrix uses its own format for storing and displaying imaging data. If you’ve already gone through the tutorials on the major fMRI software packages, such as SPM, FSL, and AFNI, you may remember that all of them can read and write images in NIFTI format. Chapter 3 of the MRtrix Tutorial of Andy's Brain Book: https://tinyurl.com/y8qn9snb Command to convert raw data to .mif format: mrconvert sub-CON02_ses-preop_acq-AP_dwi.nii.gz sub-02_dwi.mif... The B.A.T.M.A.N. tutorial, and the associated Nature Protocols paper authored by Marlene Tahedl, provides an excellent overview of a full analysis pipeline using MRtrix3, with plenty of examples, helpful strategies and advice about common pitfalls.
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