[Mrtrix-discussion] Motion correction best practise

[Donald Tournier]

Hi Ivan,

I'm probably not the best person to ask about this... There's a few other
people on this list whose opinion on the matter is much better informed
than mine, I cordially invite them all to chip in. ;)

I've no experience with ExploreDTI, but you can ask Alex Leemans directly
through the ExploreDTI mailing list. That said, I'm fairly confident it
does the b-matrix update...

As to FSL, as far as I know it also does volume-wise affine registration,
and it is possible to do the b-matrix update, although I'm not familiar
with the procedure needed to do this.

I'm not familiar with any package that does slice-by-slice registration,
but my gut feeling on the matter is that there's probably not a great deal
of point to doing this as slice-wise mis-registration is generally
accompanied by through-plane motion, which will cause signal corruption due
to spin history effects. For this reason, I'd consider the entire volume
affected to be corrupt in this case: even if there is no obvious signal
drop, the chances are there will be some corruption. That said, it might be
worth doing if your downstream processing pipeline has a way of handling
outliers, etc.

I'd also like to highlight that these approaches are still far from
perfect. I've already raised the issue on this list, but based on my
limited exposure to FSL's eddy_correct (which seems to be what most people
use), I think it often creates more problems than it solves. I hasten to
add that this problem may also apply to other approaches, but so far I've
only been exposed to data processed using eddy_correct. I've come across
many cases where the coregistration introduces artefacts, even when the
original data wasn't particularly affected in the first place. These
artefacts typically consist of the DW images being stretched along one or
more axes, probably because the algorithm tries to match the parenchyma bit
of the DW volumes to the parenchyma+CSF parts of b=0 volume. This is
particularly pronounced with high b-value data, but I've also seen it
happen in run-of-the-mill b=1000 data too (as recently as a couple of weeks
ago, in fact). All this to say, if you use these tools, please don't treat
them as a black box, do check that they're working as expected.

On the upside, Jesper Anderson recently proposed a new approach based on
Gaussian processes, which I think has now made it into FSL5. If any other
users have tried using it, feel free to comment on this...

Cheers,
Donald.



On 18 November 2013 03:06, Ivan Alvarez <ivan.alvarez.11 at ucl.ac.uk> wrote:

>  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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> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>


-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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