[Mrtrix-discussion] Motion correction best practise
Ivan Alvarez
ivan.alvarez.11 at ucl.ac.uk
Tue Nov 19 05:26:39 PST 2013
Hi Romain,
This is straying into a FSL-specific question, but I'll ask anyway since
we're on the topic - Am I correct in understanding that Eddy does a)
motion correction and b) eddy current correction in its base form, with
the optional bonus step of c) EPI distortion under Topup?
I ask because in the manual it states Topup requires your DWI data and
also a b0 volume with the opposite phase-encoded direction.
Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH
On 19/11/13 09:20, romain valabregue wrote:
> 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
>>>
>>>
>>> _______________________________________________
>>> Mrtrix-discussion mailing list
>>> Mrtrix-discussion at www.nitrc.org
>>> <mailto: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 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/
>>
>>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20131119/c94cb4a2/attachment-0001.html>
More information about the Mrtrix-discussion
mailing list