<div dir="ltr">Hi David,<div><br></div><div>I've never heard of this being referred to as a 'nubbin', but it's clear enough... ;)</div><div><br></div><div>Looking at your responses though, the 'nubbin' isn't all that worrying. What's more worrying is the fact that the lmax=6 response is sharper than the lmax=8 response, which seems wrong. Your lmax=8 response is certainly broader than I'd expect at b=3000. </div><div><br></div><div>So all this suggests that the response function estimation isn't working all that well, which is typically a symptom of a poor single-fibre mask. You used an FA threshold of 0.7 here, but bear in mind that this is by no means a 'default' - this is more of a guideline, <a href="http://jdtournier.github.io/mrtrix-0.2/tractography/preprocess.html#csd">as stated in the documentation</a>. Here's the relevant excerpt:</div><div><br></div><div><blockquote 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" class="gmail_quote">Note that this value is a guide only - feel free to use a different value if this does not produce satisfactory results. Ideally, you should now have a mask containing a few hundred voxels, all located within high FA white matter regions. <b>It is very important to check that the single-fibre mask is suitable, as otherwise the response function produced in the following step may be totally inappropriate, which would seriously affect the quality of the CSD output</b>. If needed, you can edit this mask image to remove unwanted voxels using the <a href="http://jdtournier.github.io/mrtrix-0.2/general/mrview.html#roi" style="text-decoration:none;color:teal">ROI analysis</a> sidebar tool within <a href="http://jdtournier.github.io/mrtrix-0.2/general/mrview.html" style="text-decoration:none;color:teal">MRview</a>.</blockquote></div><div><br></div><div>I would have a good look at the single-fibre mask used in this step, and check against the above. The chances are you might find a lot of noisy high-FA edge voxels got included or something, despite the erosion step. This all depends on how good the initial brain mask was (I often found it difficult to exclude the nasal sinuses, for example). Unfortunately, this step can be a bit fiddly. </div><div><br></div><div>Alternatively, you could upgrade to <a href="http://www.mrtrix.org">MRtrix3</a> - we've put in quite a bit of work on <a href="http://mrtrix.readthedocs.org/en/latest/concepts/response_function_estimation.html">estimating the response function</a>...</div><div><br></div><div>All the best,</div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 22 March 2016 at 19:47, David Grayson <span dir="ltr"><<a href="mailto:dgrayson@ucdavis.edu" target="_blank">dgrayson@ucdavis.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Hi MRtrixers,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I have HARDI datasets on a large sample of young adults (7-16yrs) taken with 72-dir and b0=3000. I am wondering whether I should proceed with lmax=6 or 8. I am using MRtrix 0.2.12.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I am concerned about using lmax=8 because in the response function there is often a ‘nubbin’ that appears right in the center of the Z-axis line that doesn’t appear at lmax=6. The below link shows an example of the RF’s generated for a
single subject taken at lmax=6 (on the left) and lmax=8 (on the right). These are generated using default parameters (FA threshold of 0.7 for the single-fiber-orientation mask).<u></u><u></u></p>
<p class="MsoNormal"><a href="http://imgur.com/a/ODrcf" target="_blank">http://imgur.com/a/ODrcf</a><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Hopefully it’s obvious what I’m talking about. Sometimes this nubbin is more pronounced than what I’m showing here. I’m not sure how concerned I should be about this, but based on my intuition about what the RF means, the Z-axis itself
should represent the global minimum of the DW signal, which is obviously not the case with lmax=8. Should I avoid any appearance of this effect at all costs, or is there some rule of thumb for how big it can be before I should be concerned about it?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks,<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></p><span class="HOEnZb"><font color="#888888">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">David<u></u><u></u></p>
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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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