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<p>Thanks for the responses here.</p>
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<p>I should have mentioned, I have been using the freesurfer WM mask (co-registered to the B0) to exclude noisy voxels. Looks like there was an issue with co-registration. Now that this is fixed, indeed the lmax=8 response looks (very slightly) sharper than
lmax=6.</p>
<p><br>
</p>
<p>However, I'm wondering if you can have a look at the following comparisons of lmax=6 vs lmax=8, using an eroded WM mask and using the full WM mask. The lmax=8 still produces the protruberance on the z-axis, which is exaggerated using the eroded WM mask.
Does this suggest that I should perhaps stick with lmax=6, and avoid eroding any further the WM mask? Would you consider these RF's acceptable now?</p>
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<p><a href="http://imgur.com/42NCktt" id="LPlnk898088" title="http://imgur.com/42NCktt
Cmd+Click or tap to follow the link">http://imgur.com/42NCktt</a><br>
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<p><span style="font-size: 12pt;">Thank you very much,</span><br>
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<p>David</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> albnet@gmail.com <albnet@gmail.com> on behalf of Dorian P. <alb.net@gmail.com><br>
<b>Sent:</b> Tuesday, March 22, 2016 3:10 PM<br>
<b>To:</b> J-Donald Tournier<br>
<b>Cc:</b> David Grayson; mrtrix-discussion@www.nitrc.org<br>
<b>Subject:</b> Re: [Mrtrix-discussion] Response functions at lmax=6 vs lmax=8</font>
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<div dir="ltr">I always used to correct manually the single fiber mask. The automatic thresholding includes out of brain voxels in inferior slices. A simple threshold is not to be trusted, I think.
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<div>Dorian</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Mar 22, 2016 at 6:01 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">Hi David,
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</div>
<div>I've never heard of this being referred to as a 'nubbin', but it's clear enough... ;)</div>
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<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" target="_blank">
as stated in the documentation</a>. Here's the relevant excerpt:</div>
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<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">
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" target="_blank" style="text-decoration:none; color:teal">ROI analysis</a> sidebar tool within <a href="http://jdtournier.github.io/mrtrix-0.2/general/mrview.html" target="_blank" style="text-decoration:none; color:teal">MRview</a>.</blockquote>
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<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>
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<div>Alternatively, you could upgrade to <a href="http://www.mrtrix.org" target="_blank">
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" target="_blank">estimating the response function</a>...</div>
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<div>All the best,</div>
<div>Donald.</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">
<div>
<div class="h5">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>
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<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<div class="h5">
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<div>
<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><font color="#888888"><u></u><u></u></font></span></p>
<span><font color="#888888">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">David<u></u><u></u></p>
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<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>
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