<div dir="ltr">Hi folks,<div><br></div><div>May I pop in a couple of related questions. First, has anyone obtained correlation between AFD and FA? I extracted once AFD/HMOA with another software (not MRtrix) and the correlation with FA was very high 0.9+. I was susprised by this at the time but didn't have time to follow up.</div><div><br></div><div>Second, pardon if I am not updated with recent development, but is multi-tissue CSD similar to NODDI? What is the difference of the two?</div><div><br></div><div>Thank you.</div><div>Dorian</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 28, 2015 at 3:42 PM, J-Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</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 class="gmail_extra"><div class="gmail_quote"><div>Hello again,</div><span><div> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div></div>I will read AFD related documentation in mrtrix3; you are right, I should move to new release, but we have data already processed with old version and doing csd fittings again would take quite long time...<br></div></div></div></blockquote><div><br></div></span><div>Well, the version of CSD in MRtrix3 is much faster - I process a typical dataset in ~15s. And with the changes we have coming up, it'll go down further to ~6s... :)</div><span><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div>After a quick look at afd paper, I have only another question for you related to rational of AFD. If you have one fiber population in a voxel its intepretation is straightforward. But, provided you have two fiber bundles "estimated" within a voxel, what could be a proper afd measure? Could average of two fod amplitudes be the answer?<br></div></div></div></blockquote><div><br></div></span><div>From my point of view, the interpretation of AFD is straightforward whether you have one or more fibre populations - it relates explicitly to each individual fibre population. I guess the issue you're having is that it's no longer a simple scalar per voxel - but then that is a clearer reflection of the reality than a simple scalar could give you. </div><div><br></div><div>However, one option that you have available to you is to use the <i>total </i>AFD - i.e. the sum of the AFDs for all fibre populations. It is clearly less informative than the AFD per fibre population (i.e. the <i>fixel-wise</i> AFD), but if you must have a scalar per voxel, it would definitely be better than the average AFD (if you have 2 fibre populations in a voxel, their average AFD will be half that of the voxel next door that contains only one of the fibre populations, which is a very artificial difference). The total AFD is trivial to compute since it's the l=0 term of the CSD output - the first volume in the file (all other harmonics have zero integral over the sphere). This measure is actually a pretty good surrogate for neurite density - with the caveat that the CSD output is not very well normalised, so care would be needed to ensure data are comparable across subjects, as for the AFD itself. If performing non-linear registration to a common space, you will also have the issue of modulation to deal with, which is not trivial since ideally you should modulate according to the change in cross-sectional area across the fibre axis (as is done in AFD). </div><div><br></div><div>So yes, there are options, but none are as simple as one might like...</div><div><br></div><div>Cheers,</div><div>Donald.</div><div><div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><br></div>Thanks again,<br></div>Alessandro<div><div><br><br><div class="gmail_extra"><br><div class="gmail_quote">2015-05-28 18:54 GMT+02:00 J-Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Alessandro,</p>
<p dir="ltr">Well, at heart AFD really is only the amplitude of the FOD along the fibre direction of interest - actually, technically it's the integral of the FOD over the FOD peak. You can compute the FOD amplitude in the old version, but all the tools to compute the integral are in MRtrix3...</p>
<p dir="ltr">Besides, to really do AFD justice requires some fairly complex preprocessing steps to ensure values can be compared across subjects, which we still haven't documented properly. They're all currently implemented in MRtrix3 - this is where all the development effort is going. While you probably could hack something together using the old version, my recommendation would be to upgrade and wait for the documentation to be updated (hopefully not too long after the ISMRM...).</p>
<p dir="ltr">Even if you do want to stick with the old version, the steps required will at least be documented on the MRtrix3 wiki, so you'll be able to see for yourself how feasible this might be...</p>
<p dir="ltr">Cheers,<br>
Donald</p><div><div>
<div class="gmail_quote">On 28 May 2015 5:41 pm, "Alessandro Calamuneri" <<a href="mailto:alecalamuneri@gmail.com" target="_blank">alecalamuneri@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Hi Donald,<br></div>thanks for quick answering..<br>Given I am using old mrtrix version (0.2), what could be a pipeline for calculating AFD?<br><br></div><div>Thanks,<br></div><div>Alessandro<br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-05-28 18:03 GMT+02:00 J-Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Alessandro,</p>
<p dir="ltr">Yes, that particular question has come up many times over the years... I think we have a suitable answer now: apparent fibre density (<a href="http://www.ncbi.nlm.nih.gov/pubmed/22036682" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/22036682</a>). And this will probably be improved further using multi-tissue CSD (<a href="http://www.ncbi.nlm.nih.gov/pubmed/25109526)." target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/25109526).</a>..</p>
<p dir="ltr">Hope this answers your question.<br>
Cheers,<br>
Donald</p>
<div class="gmail_quote"><div><div>On 28 May 2015 4:00 pm, "Alessandro Calamuneri" <<a href="mailto:alecalamuneri@gmail.com" target="_blank">alecalamuneri@gmail.com</a>> wrote:<br type="attribution"></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div>Hi mrtrix experts,<br><br></div>I would like to know whether there exists a csd based measure that might be considered the equivalent of Fractional Anisotrpy.<br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><br></div><div>Best Regards,<br></div><div>Alessandro<br></div><div dir="ltr"><div><br></div></div></div></div></div></div>
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</blockquote></div></div></div><span><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div><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> <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">+44 (0)20 7188 7118 ext 53613</a></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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