Dear MRtrix experts,
I was wondering if there is any option to plot the total motion along the x, y and z axes in mm, both relative and absolute, as it is usually done for fMRI?
Welcome Alex!
There is; but primary thanks to the efforts of others.
The MRtrix3 script dwifslpreproc includes the command-line options -eddyqc_text and -eddyqc_all. When utilised, they will take the various outputs generated by FSL’s eddy command (only the text-based files, or all files including images, respectively), and write them to a directory for you. In addition, if your system has EddyQC available (whether installed explicitly in conjunction with FSL5, or bundled with FSL6), dwifslpreproc will also execute that tool, and write the PDF that it generates to the same output directory. The EddyQC manuscript shows some of the outputs that it generates.
Cheers
Rob