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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>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> mrtrix-discussion-bounces@www.nitrc.org <mrtrix-discussion-bounces@www.nitrc.org> on behalf of Ivan Alvarez <ivan.alvarez.11@ucl.ac.uk><br>
<b>Sent:</b> 19 November 2013 13:26<br>
<b>To:</b> mrtrix-discussion@www.nitrc.org<br>
<b>Subject:</b> Re: [Mrtrix-discussion] Motion correction best practise</font>
<div> </div>
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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 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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Hope this clarifies the state of b-matrix rotation in FSL.</div>
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Cheers,</div>
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Ben</div>
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<div>-<br>
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<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>
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<div><font size="1">Phone: +32 3 265 24 77</font></div>
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ben.jeurissen@ua.ac.be</a></font></div>
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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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<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 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>
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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 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
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<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 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>
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