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<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2>Hi Usha,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2>Because we have been using DtiStudio for many fixed mouse
brains and fiber tracking results can correctly follow the small convoluted
paths of their white matter tracts, I think the algorithm should be working
without, at least, a large amount of inaccuracy.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2>DtiStudio does not keep tracking results if they are only
few pixel long. That is why you sometimes don't see tracking
results.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2>For your data, the first thing you want to check is the
SNR. Please look at the color map of your capilary phantom. Because the capilary
is aligned along Z, they should look blue. If they look noisy and not pure
blue, then SNR could be the culprit. Please also look at your vector image.
You can place your cursor in the capilary, right click, and see pixel values of
neiboring pixels. In this way, you can see FA values and vector values and
understand which threshold came in to prevent you from seeing long fibers. With
FA around 0.2, you need to have very high SNR to perform long-distance
tracking.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2>Regards,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=015571723-16022009><FONT face=Arial
color=#0000ff size=2>Susumu</FONT></SPAN></DIV><BR>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <B>On Behalf Of </B>Usha
Sinha<BR><B>Sent:</B> Monday, February 09, 2009 2:38 PM<BR><B>To:</B>
mristudio-users@mristudio.org<BR><B>Subject:</B> [Mristudio-users] fiber
tracking capillary phantom<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV>Hi <BR>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).<BR>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.<BR>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:<BR>A: Tracking condition: FA threshold: 0.15,
angle threshold: 10 degree<BR>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</DIV>
<DIV>and neighbor voxels have values of FA above threshold) <BR>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. </DIV>
<DIV><BR>B: Tracking condition: FA threshold: 0.15, angle threshold: 70
degree<BR>The number of fibers are many more for this condition still fiber
length does not reach 5 cm average (more like 3 cm)!<BR> <BR>My
questions::<BR>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)<BR>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.<BR>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<BR> <BR>This has been of great
concern-- please do send me some feedback<BR>usha sinha<BR><A
href="mailto:usinha@sciences.sdsu.edu">usinha@sciences.sdsu.edu</A><BR><A
href="mailto:usinhaster@gmail.com">usinhaster@gmail.com</A></DIV></BODY></HTML>