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<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 (
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY">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
cite="mid:CAHgym8LX=fpCcXpDfg8qY0fH8wtJS7KTpU1XndKWU=q736Nirw@mail.gmail.com"
type="cite">
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<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" text="#000000"> 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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</blockquote>
</div>
<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>
<div>
<i><font color="#990000">Division of Imaging Sciences &
Biomedical Engineering<br>
King's College London</font></i>
<div><i><font color="#990000"><br>
</font></i></div>
<div><i><font color="#990000"><b
style="font-family:Calibri,sans-serif;font-size:15px"><span
style="font-size:10pt">A:</span></b><span
style="font-family:Calibri,sans-serif;font-size:10pt"> Department
of Perinatal Imaging & Health, 1<sup>st</sup> Floor
South Wing, St Thomas' Hospital, London. SE1 7EH</span><br>
</font></i></div>
<div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118
ext 53613</font></i></div>
</div>
<div><i><font color="#990000"><b>W:</b> <a
moz-do-not-send="true"
href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering"
target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br>
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