<div dir="ltr"><div><div><div><div>Hi Scott,<br><br></div>The FOD amplitude cutoff reflects the specific amplitude of the FOD along the direction considered, i.e. it takes into account all SH coefficients of the FOD to evaluate it's true amplitude along a specific direction. As such, it's not simply a spatial mask that limits the tracks to some spatial regions, but actually a full 5D spatio-angular mask! The fact that you encounter this specifically for subjects with enlarged ventricles (i.e. not for others), sounds a bit mysterious to me... Maybe I'm overlooking some simple explanation here... :-) Do you have some clear images/screenshots that illustrate this happening with the patients (but not with the other subjects)? A screenshot of some tracks overlaid on the FODs might be helpful.<br>
<br></div>For the second question: I've always assumed the angular tolerance directly specified how much the initial direction could deviate from the desired one. I.e., that would mean it's the angular radius of the cone. But now that you mention it, I'm actually not fully sure: the documentation is indeed a bit ambiguous on this one. It's at least a good candidate for clarification in the manual. :-) A very rough and quick look in the source code shows a dot product between both directions somewhere. This also seems to indicate it will be the radius of the cone (i.e. the maximum angle between both directions<br>
</div>). But since I didn't fully check all related code, don't take my word on it... :-) Maybe someone else can confirm/reject this?<br><br></div>Hope this already helps a bit!<br><br>Cheers,<br>Thijs<br></div>
<div class="gmail_extra"><br clear="all"><div><div dir="ltr"><span style="color:rgb(68,68,68)"><b><font size="4">Thijs Dhollander</font><br><font><a href="mailto:thijs.dhollander@gmail.com" target="_blank">thijs.dhollander@gmail.com</a><br>
Tel. +32 475 36 44 27</font></b><br><font size="1">Medical Image Computing (MIC), ESAT-PSI, Department of Electrical Engineering, KU Leuven</font></span></div></div>
<br><br><div class="gmail_quote">On Tue, Sep 24, 2013 at 2:43 AM, 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">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Hi Donald.</div>
<div><br>
</div>
<div>Two questions:</div>
<div>First, I've been doing some tractography of the optic radiations. The tracks are good in most subjects. However in some patients with enlarged ventricles the tracks tend to cut through the ventricles. My understanding of the FOD amplitude cutoff is that
it reflects the amplitude of the first component. Is that correct? </div>
<div>Second, with the –indirection flag, is the angular tolerance the angular radius or diameter of the cone around the starting direction?</div>
<div><br>
</div>
<div>Many thanks</div><span class="HOEnZb"><font color="#888888">
<div>Scott</div>
<div><br>
</div>
</font></span></div>
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