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<div class="moz-cite-prefix">Hello,<br>
<br>
the artefact added with eddy_correct is more pronounce for high
bvalue (3000) with 1000 or 1500 it should go better<br>
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 <br>
<br>
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.<br>
<br>
I hope it helps <br>
<br>
Romain<br>
<br>
Le 18/11/2013 23:39, Jeurissen Ben a écrit :<br>
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Hi all,</div>
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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.</div>
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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.</div>
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Hope this clarifies the state of b-matrix rotation in
FSL.</div>
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<br>
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Cheers,</div>
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Ben</div>
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<div>-<br>
<div>
<div>
<div>
<div>
<font size="1">Ben Jeurissen, Ph.D.</font></div>
<div>
<div><font size="1">Post-doctoral researcher</font></div>
<div><font size="1">Vision Lab, Dept. of
Physics</font></div>
<div><font size="1">University of Antwerp</font></div>
<div><font size="1">Universiteitsplein 1,
N.1.18</font></div>
<div><font size="1">B-2610 Wilrijk, Belgium</font></div>
<div><font size="1">Phone: +32 3 265 24 77</font></div>
<div><font size="1">Email:
<a class="moz-txt-link-abbreviated" href="mailto:ben.jeurissen@ua.ac.be">ben.jeurissen@ua.ac.be</a></font></div>
<div><font size="1">Url: <a
moz-do-not-send="true"
title="http://visielab.ua.ac.be/people/ben-jeurissen
Ctrl+Click to follow link"
href="http://visielab.ua.ac.be/people/ben-jeurissen"
target="_blank">http://visielab.ua.ac.be/people/ben-jeurissen</a></font></div>
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<hr tabindex="-1">
<div id="divRpF964956" style="direction: ltr;"><font
color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a>
[<a class="moz-txt-link-abbreviated" href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a>] on behalf of
Ivan Alvarez [<a class="moz-txt-link-abbreviated" href="mailto:ivan.alvarez.11@ucl.ac.uk">ivan.alvarez.11@ucl.ac.uk</a>]<br>
<b>Sent:</b> 18 November 2013 13:31<br>
<b>To:</b> Donald Tournier<br>
<b>Cc:</b> mrtrix mailinglist<br>
<b>Subject:</b> Re: [Mrtrix-discussion] Motion correction
best practise<br>
</font><br>
</div>
<div>
<div class="moz-cite-prefix">Hi Donald,<br>
<br>
Thank you for all your comments. <br>
<br>
I was not aware FSL did b-matrix update, will definitely
look into this. <br>
<br>
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?<br>
<br>
PS The Gaussian process code is now in FSL under the name
EDDY ( <a moz-do-not-send="true"
href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY"
target="_blank">
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY</a>). I
haven't personally tried it, but would love to hear from
other users!<br>
<pre class="moz-signature" cols="72">Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH</pre>
On 18/11/13 12:15, Donald Tournier wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Ivan,
<div><br>
</div>
<div>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. ;)</div>
<div><br>
</div>
<div>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...</div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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...</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Donald.</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 18 November 2013 03:06, Ivan
Alvarez <span dir="ltr">
<<a moz-do-not-send="true"
href="mailto:ivan.alvarez.11@ucl.ac.uk"
target="_blank">ivan.alvarez.11@ucl.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex; border-left:1px #ccc solid; padding-left:1ex">
<div bgcolor="#FFFFFF">Hi Donald,<br>
<br>
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.<br>
<br>
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:<br>
<br>
ExploreDTI<br>
* Affine registration<br>
* Whole volume at a time<br>
* Updates B-matrix<br>
<br>
FSL<br>
* Affine registration<br>
* Slice-by-slice<br>
* Does<i> not</i> update B-matrix<br>
<br>
>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 (<a moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/pubmed/19319973"
target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/19319973</a>).
Is this roughly correct? If so, are there any
other considerations specific to MRtrix?<span
class="HOEnZb"><font color="#888888"><br>
<pre cols="72">--
Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH </pre>
</font></span></div>
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-- <br>
<div dir="ltr"><b><font color="#990000">Dr J-Donald
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<div><font color="#990000"><br>
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