<div dir="ltr">Hi Scott, <div><br></div><div>Yes, the T2 shine-through is one of those issues that also puzzles me. I'm not sure how best to handle it. If the high T2 could be assumed to arise purely from increased free water, it would have CSF-like properties, and hence contribute very little to the high b-value image, so all would be good. But genuine shine-through still shows up with high signal in the DWI, so there must be some other explanation. Unfortunately I've not had a chance to really dig into the histology literature to figure out what might actually be causing this. </div><div><br></div><div>In terms of how to handle this within MRtrix, you can use the multi-tissue CSD algorithm that's <a href="https://plus.google.com/101826858124420446685/posts/QhYaHLGcdmN">recently been made available</a> within <a href="https://github.com/MRtrix3/mrtrix3/wiki">MRtrix3</a> (although we need to tidy a few things up on that front) to decompose your data into CSF and tissue components (it won't be perfect with only 2 compartments, but it'll do a decent job of removing the CSF signal from the FOD). However, this won't necessarily help you since the areas you're concerned about probably don't have a lot of CSF-like signal, and the output of the multi-tissue CSD is also not normalised to the b=0, so you'd probably get very similar results to what you already have... </div><div><br></div><div>Daan Christiaens showed recently that <a href="https://lirias.kuleuven.be/bitstream/123456789/496046/3/MICCAI2015_CNSF_camready.pdf">multi-tissue CSD running with 4 compartments</a> (WM, GM, CSF + edema) might allow edema to be distinguished from free water (see Figure 6 in particular). But this needs a 4 b-value (b=0 + 3 shells) sequence, which you don't have... But the point here is that the signal from this particular pathology is clearly distinct from that of CSF.</div><div><br></div><div>So the question then becomes whether normalising to the b=0 is the right thing to do in principle, even if the CSF signal weren't a problem. I think if you do the maths, you'll find it's not as simple as it might seem, for exactly the same reasons I've given previously regarding CSF contamination. Consider a voxel containing 50% WM, 50% 'pathology', i.e. whatever is causing the shine-through, be it edema or something more complex (maybe demyelination is also contributing in MS...?). The raw DW signal (and hence the FOD, given the linearity of the operation) would essentially be the linear sum of the DWI signal from the two compartments, which means there would be a large amount of contamination from the shine-through, presumably leading to a drastic increase in noise for the FOD, along with a increased isotropic component (assuming the shine-through signal is not directional - not sure how true that is). The main point though is that the WM part of that FOD should be appropriately scaled. If you normalised to the b=0 signal, you'd be computing: S = ( ½DW_WM + ½DW_ST ) / (½b0_WM + ½b0_ST) - so just like in the case of CSF, assuming b0_ST >> b0_WM, what this essentially accomplishes is a large overall reduction in the FOD amplitude, WM and edema alike. The amount of contamination would be the same relative to the FOD amplitude, but the FOD would be strongly attenuated if normalising to the b=0. This might look cleaner, but it would definitely cause the tractography to struggle or fail outright if trying to track through such regions, even though there may be significant amount of genuine WM present. Depending on your particular question, this may or may not be a bias you can live with... Either way, the tracking would struggle, due to large amounts of contamination when <i>not </i>normalised, or due to very low FOD amplitudes when normalised.</div><div><br></div><div>So I don't how you could somehow remove the edema signal from the DWI signal using 2 b-values only. It <i>might</i> be possible to perform some kind of partial volume correction <i>if</i> you had an independent estimate of the partial volumes, but this sounds far from trivial to do robustly. Maybe Thijs can do some magic here - I'd definitely recommend you take him up on his offer and have that coffee...</div><div><br></div><div>Cheers,</div><div>Donald.</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 20 January 2016 at 06:59, Thijs Dhollander <span dir="ltr"><<a href="mailto:thijs.dhollander@florey.edu.au" target="_blank">thijs.dhollander@florey.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Hi Scott,<br><br></div>Interesting issue this is indeed! So to summarise what you are reporting (just to make sure I'm getting it right): you're seeing hyperintense voxels at b=3000 in the MS lesion, but the ADC map shows no clear decrease in values compared to surrounding (supposedly healthy) WM tissue, is that correct? Are you sure there's not even a slight decrease in ADC? Due to the log-transform, it might be hard to spot; definitely try to increase the contrast in your viewer to investigate the area. I'm not an expert on MS, but doing a few searches, I seem to run into articles describing actual increased restriction in certain (stages of) MS lesions (presenting ADC maps with hypointense lesions.<br><br></div>Let's say you would indeed be observing no decrease in ADC at all, yet a clear increase in b=3000 DWI values, that would mean an obvious increase in value of the b=0 image(s): are you seeing that as well in the data at hand?<br><br></div>If the latter is true, I think I can potentially help you out with these partial volume issues (over time). I notice you're at Unimelb. I'm working at the Florey (in Heidelberg, but mobile and in the Parkville area at times); we should have a coffee and a chat some time, and take a good hands-on look at those data you're sitting on. ;-)<br><br></div>Cheers,<br></div>Thijs<div><div class="h5"><br><div><div><div><div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On 20 January 2016 at 14:54, Scott Cameron Kolbe <span dir="ltr"><<a href="mailto:kolbes@unimelb.edu.au" target="_blank">kolbes@unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Donald, Rob and Dave<br>
<br>
Just found this discussion whilst going through the archives. Sorry to bring it up again but I’ve been having similar concerns to Jan recently whilst working on multiple sclerosis data. The T2 “shine-through” effect that Jan is referring to in MS results from T2 signal enhancement that is not related to changes in CSF volume fraction. Therefore hyperintense voxels in DWI, considered by SD to be highly restricted diffusion, are in fact not that different from surround tissue on the ADC map.<br>
<br>
This problem might be solved by acquiring low-B images for normalisation where freely diffusing fluid is essentially annulled but even lightly restricted water is not. However, we are sitting on quite a bit of data with only b=0 or b=3000. Do you think partial volume correction might be possible?<br>
<br>
cheers<br>
Scott<br>
<br>
<br>
Scott Kolbe<br>
<a href="mailto:kolbes@unimelb.edu.au" target="_blank">kolbes@unimelb.edu.au</a><br>
<br>
<br>
<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><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></div></div></div>
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