Automated quality check

Hello MRtrix3 community,

I am currently discovering DTI preprocessing and MRtrix3.
I have a “basic” question for MRtrix3 usage.
Is there a way to produce an automated quality check in order to detect putative outliers with MRtrix3?
or is there a way to easily plot motion, index of signal homogeneity, SNR?

Thank you!

Welcome Clément!

Since the bulk of DWI pre-processing relevant to these kinds of parameters is still principally deferred to FSL commands via the wrapper script dwifslpreproc, the metrics yielded by those commands is probably the first port of call. If you run dwifslpreproc with one of the “-eddyqc_*” command-line options, then not only will you get the various files generated by FSL eddy, but (if installed) it will also run EddyQC, which gives summary measures of things like motion and prevalence of outliers.

SNR is a difficult one to answer, since there is no consensus on exactly what measure should be referred to as such derived in the context of DWI. The dwidenoise command with the -noise option gives an estimate of the noise level, which may be of use. If you want to estimate SNR in a specific way though, it’s just a matter of breaking the calculation up into its constituent components and knowing the relevant MRtrix3 commands.