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<div class="moz-cite-prefix">Hi Jonathan,<br>
<br>
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!<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 02/12/2013 10:20, Ashmore, Jonathan wrote:<br>
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<p>Hi Ivan,</p>
<p>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. </p>
<p><br>
</p>
<p>I hope that's useful</p>
<p>Jonathan</p>
<div>
<p><br>
</p>
<div><font face="Tahoma" size="2">MRI Physicist</font></div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
color="#000000" face="Calibri, sans-serif"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:mrtrix-discussion-bounces@www.nitrc.org">mrtrix-discussion-bounces@www.nitrc.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:mrtrix-discussion-bounces@www.nitrc.org"><mrtrix-discussion-bounces@www.nitrc.org></a> on behalf
of Ivan Alvarez <a class="moz-txt-link-rfc2396E" href="mailto:ivan.alvarez.11@ucl.ac.uk"><ivan.alvarez.11@ucl.ac.uk></a><br>
<b>Sent:</b> 19 November 2013 13:26<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a><br>
<b>Subject:</b> Re: [Mrtrix-discussion] Motion correction
best practise</font>
<div> </div>
</div>
<div>
<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 type="cite">
<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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<br>
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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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<br>
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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
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title="http://visielab.ua.ac.be/people/ben-jeurissen
Ctrl+Click to follow link"
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target="_blank">http://visielab.ua.ac.be/people/ben-jeurissen</a></font></div>
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<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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<div dir="ltr"><b><font color="#990000">Dr
J-Donald Tournier (PhD)</font></b><br>
<div><font color="#990000"><br>
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