<div dir="ltr">OK, that makes sense. Unfortunately it's really important to check the voxels from the SF mask, since there are so many ways that bad ones can creep in. As to the effect of a low response function, this will result in correspondingly large FODs, and will mean that the default 0.1 cutoff used for tractography will effectively be smaller than expected, allowing the algorithm to follow more noisy and potentially spurious low-intensity FOD peaks. Best to make sure it's properly scaled...<div>
<br></div><div>Cheers,</div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 28 October 2013 16:47, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@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">The single fiber mask contains voxels out of brain, from skull etc. I will make some attempts to better refine the DWI mask up in the processing pipeline.<div>
<br></div><div>However, I still see good fiber tractography. What is the effect of low response function on CSD results?</div>
<div><br></div><div>Yes, this is a healthy control.</div><div><br></div><div>You help is appreciated.</div><div>Thank you</div><span class="HOEnZb"><font color="#888888"><div>Dorian</div></font></span></div><div class="HOEnZb">
<div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">2013/10/28 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"><div dir="ltr">Hi Dorian,<div><br></div><div>That's a bit lower than I'd expect, I typically see about 3/4 of the b=0 intensity (I think). That's for a b-value of ~3000, I would expect it to be lower than that for higher b-values. Basically, the first term in the response function multiplied by ~0.28 should correspond to the mean DW intensity averaged over all orientations. If that's not the case, I would have a good look at your single-fibre mask (the mask from which you estimate the response function), to make sure that all voxels included are in sensible, single-fibre, pure WM locations. I also assume this is a healthy volunteer? Otherwise T2 hyperintensity could explain this. If none of this helps, maybe you can post an image of the response function, its coefficients, and the b-value, SNR and number of directions of the data set, just in case we can spot anything obvious from them...</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On 25 October 2013 16:21, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span> wrote:<br>
</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">Hi again MRtrix group,<div><br></div><div>My processing works fine and I see the doughnut shape of the response function. On checking some quality parameters I noticed that my response function starts from ~110 while white matter values on b0 are around 350-450. Is this normal or should I look at anything to improve?</div>
<div><br></div><div>This is not just a case as I have two HARDIs from the same subject, both around those values.</div><div><br></div><div>Thank you.</div><div><br></div><div>Dorian</div><div>TJU</div></div>
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<br></blockquote></div><span><font color="#888888"><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>
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</div></div></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>
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