<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 .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 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></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 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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