[Mristudio-users] fiber tracking capillary phantom

[Usha Sinha]

Hi
I have been using DTIStudio for a while for tracking fibers in muscle.
Muscle fiber FA values are lower than white matter ( in the range 0.2-0.4).
I am currently evaluating with a capillary phantom with an FA of 0.20.  This
is a straight 5 cm capillary imaged with the capillary axis along the
z-axis.
I am trying to check the SNR conditions, as well geometry parameters that
provide an accurate estimate of the capillary length.  Slice by slice
evaluation of the capillary region clearly gives a value of +_2 degrees to
the z-axis for the leading eigenvector.  So our SNR is sufficient to give
the correct lead eigenvector orientation but the tracking results are
surprising:
A: Tracking condition:  FA threshold: 0.15, angle threshold: 10 degree
1) if a seed point of 1 voxel is used, the fibers are either short or there
are often no fibers tracked from the seed point (even though seed point
and neighbor voxels have values of FA above threshold)
2) if the entire capillary array is selected,  then there are some fibers
yet average length of fibers is 2 cm (and not 5 cm as expected).  I guess
the difference between 1 and 2 is that in (2) several multiple connections
are found by the 'brute force' methods.

B: Tracking condition:  FA threshold: 0.15, angle threshold: 70 degree
The number of fibers are many more for this condition still fiber length
does not reach 5 cm average (more like 3 cm)!

My questions::
1) Why are the fibers not tracked for 10 degree angle threshold?  These are
straight capillaries with angle differences only arising from noise (which
our measurements show are within 2-3 degrees)
2) Examining fibers from a single seed point, we see that fibers are not
entirely parallel to the capillary axis; rather short segments and curvature
of fiber is seen.
3) Is there a restriction on how anisotropic the slice voxel can be:  we
have in-plane of 0.3125x0.3125 and thickness of 5mm--- however capillary
axis is along the slice axis.  I wonder of this affects the interpolation
needed for FACT

This has  been of great concern-- please do send me some feedback
usha sinha
usinha at sciences.sdsu.edu
usinhaster at gmail.com
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