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<div class="moz-cite-prefix">Hi Romain,<br>
<br>
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? <br>
<br>
I ask because in the manual it states Topup requires your DWI data
and also a b0 volume with the opposite phase-encoded direction.<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 19/11/13 09:20, romain valabregue wrote:<br>
</div>
<blockquote cite="mid:528B2D45.4040608@upmc.fr" type="cite">
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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>
</div>
<blockquote
cite="mid:384E4D541D819449ABBBD507434317D190F0B7A6@xmail34.ad.ua.ac.be"
type="cite">
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<div style="font-family:Tahoma; font-size:13px">
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<div style="widows:2; text-transform:none;
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font-family:Tahoma; white-space:normal; orphans:2;
word-spacing:0px"> Hi all,</div>
<div style="widows:2; text-transform:none;
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</div>
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font-size:13px; line-height:normal;
font-family:Tahoma; white-space:normal; orphans:2;
word-spacing:0px"> 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>
<div style="widows:2; text-transform:none;
text-indent:0px; letter-spacing:normal;
font-style:normal; font-variant:normal;
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</div>
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font-style:normal; font-variant:normal;
font-size:13px; line-height:normal;
font-family:Tahoma; white-space:normal; orphans:2;
word-spacing:0px"> 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>
<div style="widows:2; text-transform:none;
text-indent:0px; letter-spacing:normal;
font-style:normal; font-variant:normal;
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word-spacing:0px"> <br>
</div>
<div style="widows:2; text-transform:none;
text-indent:0px; letter-spacing:normal;
font-style:normal; font-variant:normal;
font-size:13px; line-height:normal;
font-family:Tahoma; white-space:normal; orphans:2;
word-spacing:0px"> Hope this clarifies the state of
b-matrix rotation in FSL.</div>
<div style="widows:2; text-transform:none;
text-indent:0px; letter-spacing:normal;
font-style:normal; font-variant:normal;
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font-family:Tahoma; white-space:normal; orphans:2;
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</div>
<div style="widows:2; text-transform:none;
text-indent:0px; letter-spacing:normal;
font-style:normal; font-variant:normal;
font-size:13px; line-height:normal;
font-family:Tahoma; white-space:normal; orphans:2;
word-spacing:0px"> Cheers,</div>
<div style="widows:2; text-transform:none;
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word-spacing:0px"> Ben</div>
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</div>
<div style="widows:2; text-transform:none;
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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
moz-do-not-send="true"
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>
</div>
</div>
</div>
</div>
</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
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a>
[<a moz-do-not-send="true"
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 moz-do-not-send="true"
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>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr"><b><font color="#990000">Dr J-Donald
Tournier (PhD)</font></b><br>
<div><font color="#990000"><br>
</font></div>
<i><font color="#990000">Senior Lecturer, </font></i><i><font
color="#990000">Biomedical Engineering</font></i>
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