[Mrtrix-discussion] tracks not terminating within sub-cutoff voxels

[Thijs Dhollander]

Hi Scott,

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.

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
).  But since I didn't fully check all related code, don't take my word on
it... :-)  Maybe someone else can confirm/reject this?

Hope this already helps a bit!

Cheers,
Thijs

*Thijs Dhollander
thijs.dhollander at gmail.com
Tel. +32 475 36 44 27*
Medical Image Computing (MIC), ESAT-PSI, Department of Electrical
Engineering, KU Leuven


On Tue, Sep 24, 2013 at 2:43 AM, Scott Cameron Kolbe
<kolbes at unimelb.edu.au>wrote:

>  Hi Donald.
>
>  Two questions:
> 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?
> Second, with the –indirection flag, is the angular tolerance the angular
> radius or diameter of the cone around the starting direction?
>
>  Many thanks
> Scott
>
>
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