[Mrtrix-discussion] Motion correction best practise
Ivan Alvarez
ivan.alvarez.11 at ucl.ac.uk
Mon Dec 2 03:02:08 PST 2013
Hi Jonathan,
Thank you for the info, I recently had a very similar experience with a
b=1000 dataset, so it's good to know these things are reproducible!
--
Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH
On 02/12/2013 10:20, Ashmore, Jonathan wrote:
>
> Hi Ivan,
>
> Just to add since you specifically asked. I have recently tried
> eddy_correct and eddy on a b=1500 data set. eddy_correct gave poor
> results and as Donald suggested introduced artefacts where the images
> were stretched along the AP direction to a far greater extent than the
> raw data. My data had motion artefact during the acquisition so I
> tried eddy and this worked really well - it corrected the motion
> without introducing the stretching. It takes significantly longer
> though than eddy_correct.
>
>
> I hope that's useful
>
> Jonathan
>
>
> MRI Physicist
> Kings College Hospital
> Ruskin Wing
> Denmark Hill
> London SE5 9RS
> Ph (KCH): 020 3299 9000 (x4898)
> Ph (CNS): 020 3228 3081
> fax (CNS): 020 3228 2116
>
>
> ------------------------------------------------------------------------
> *From:* mrtrix-discussion-bounces at www.nitrc.org
> <mrtrix-discussion-bounces at www.nitrc.org> on behalf of Ivan Alvarez
> <ivan.alvarez.11 at ucl.ac.uk>
> *Sent:* 19 November 2013 13:26
> *To:* mrtrix-discussion at www.nitrc.org
> *Subject:* Re: [Mrtrix-discussion] Motion correction best practise
> 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
>>>>
>>>>
>>>> _______________________________________________
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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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