[Mrtrix-discussion] Motion correction best practise

Tue Nov 19 01:20:05 PST 2013

Hello,

the artefact added with eddy_correct is more pronounce for high bvalue 
(3000) with 1000 or 1500 it should go better
For the bvec correction it is a tiny effect so it does not matter that 
much, (that's why it is not in there priority list), if you run 
eddy_correct you can use the extra script fdt_rotate_bvecs

The eddy procedure is much better : this is mainly because in addition 
to motion it also correct the distorsion due to eddy current. (and also 
EPI distorsion with topup). The main limitation is that it require a 
specific acquisition (either the direction have to be over the all 
sphere or you need each direction with direct and oposite phase 
direction), but It worth to change your dwi acquisition.

I hope it helps

Romain

Le 18/11/2013 23:39, Jeurissen Ben a écrit :
> Hi all,
>
> FSL's "eddy_correct" doesn't do b-matrix rotation. They do offer a 
> separate script to reorient the bvecs file after running eddy_correct, 
> though.
>
> FSL5's "eddy" doesn't do b-matrix rotation either and there is no 
> script available to reorient the bvecs file. On their mailinglist the 
> developers stated developing such a tool is currently not high on 
> their priority list.
>
> Hope this clarifies the state of b-matrix rotation in FSL.
>
> Cheers,
> Ben
>
> -
> Ben Jeurissen, Ph.D.
> Post-doctoral researcher
> Vision Lab, Dept. of Physics
> University of Antwerp
> Universiteitsplein 1, N.1.18
> B-2610 Wilrijk, Belgium
> Phone: +32 3 265 24 77
> Email: ben.jeurissen at ua.ac.be
> Url: http://visielab.ua.ac.be/people/ben-jeurissen
> ------------------------------------------------------------------------
> *From:* mrtrix-discussion-bounces at public.nitrc.org 
> [mrtrix-discussion-bounces at public.nitrc.org] on behalf of Ivan Alvarez 
> [ivan.alvarez.11 at ucl.ac.uk]
> *Sent:* 18 November 2013 13:31
> *To:* Donald Tournier
> *Cc:* mrtrix mailinglist
> *Subject:* Re: [Mrtrix-discussion] Motion correction best practise
>
> Hi Donald,
>
> Thank you for all your comments.
>
> I was not aware FSL did b-matrix update, will definitely look into this.
>
> It's interesting that you mention we may be loosing more than we are 
> gaining with motion correction, particularly with the introduction of 
> artefacts and poor registration at high b-values. Is there a rule of 
> thumb for when are such procedures useful/detrimental? For example, in 
> fMRI movement >5mm within a single run (i.e. 5-10 minutes continuous 
> scanning) is considered worrisome but salvageable and >10mm is often 
> too much to be rescued by registration. Is there something like that 
> for dMRI?
>
> PS The Gaussian process code is now in FSL under the name EDDY ( 
> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY 
> <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY>). I haven't personally 
> tried it, but would love to hear from other users!
> Kind regards,
> Ivan Alvarez
>
> PhD Candidate
> Imaging and Biophysics Unit
> UCL Institute of Child Health
> 30 Guilford Street, London, WC1N 1EH
> On 18/11/13 12:15, Donald Tournier wrote:
>> 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 
>> <mailto: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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>>
>>
>>
>>
>> -- 
>> *Dr J-Donald Tournier (PhD)*
>>
>> /Senior Lecturer, //Biomedical Engineering/
>> /Division of Imaging Sciences & Biomedical Engineering
>> King's College London/
>> /
>> /
>> /*A:* Department of Perinatal Imaging & Health, 1^st  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/
>
>
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