[Mrtrix-discussion] Motion correction best practise

[Ivan Alvarez]

Hi Donald,

I wanted to bring up motion correction again, particularly what is 
recommended for and against in MRtrix. I am aware the issue has been 
raised in the mailing list before, but it might be useful to have an 
idea of what is generally a good or bad idea.

So far, I have seen people doing motion/eddy-current correction in 
either ExploreDTI or FSL. The documentation for both is these is 
somewhat scant and I am trying to piece together what do they exactly 
do. This is my naive reading so far, please feel free to correct me:

ExploreDTI
* Affine registration
* Whole volume at a time
* Updates B-matrix

FSL
* Affine registration
* Slice-by-slice
* Does/not/ update B-matrix

 From what I understand in the discussion, the slice-by-slice 
registration is preferable to avoid smearing artefacts across the whole 
volume while updating the B-matrix can generally improve results 
(http://www.ncbi.nlm.nih.gov/pubmed/19319973). Is this roughly correct? 
If so, are there any other considerations specific to MRtrix?

-- 
Kind regards,
Ivan Alvarez

PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH

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