DWIEddyCorrectMI -p -m transformfile dwi.nii.gz dwi_mc.nii.gz 0
- -p enables parallel execution (optional)
- -m specifies an output file for saving estimated transforms. Useful as a motion estimate.
- dwi.nii.gz is the image file to be motion corrected
- dwi_mc.nii.gz is the output, corrected image file
- 0 is the index of the image used as the reference in registration
Note that the order of parameters is important, with -p and -m appearing first, if used.