Hi Yi,<br><br>I want to hear from Hangyi for detailed response, but there are known issues in tensor fitting. In the linear tensor fitting, we assume that the tensor has positive diagonal elements. This means, for example, when gradients are applied (diffusion-weighted), signal becomes lower than non-weighted images (b0). However, there are situation when this assumption is violated. At the edge of the brain, subject motion (non-reproducible) and eddy current (reproducible) causes pixel mis-registration, meaning, the pixel is sometimes inside and sometime outside the brain. Then the fitting blows up. Also, for the very highly anisotropic area such as CC, DWIs with the gradients applied perpendicular to the fiber (say, we expect only 5% signal loss) could have higher intensity than b0 due to SNR (say more than 5% signal fluctuation). In this case, the fitting blows up again.<br>
<br>In these situations, it is not uncommon to get negative diagonal elements or FA higher than 1.0. To prevent this, there are several proposed methods. I believe DtiStudio simply replace the negative diagonal elements with 0. <br>
<br>The issues of the CC should be reduced if you have higher SNR (or more DWIs). What is the resolution and the number of DWIs you are using?<br>For the brain edge, please check the fitting error map based on the DtiStudio Updage file I recently distributed.<br>
<br>Susumu<br><br><div class="gmail_quote">On Wed, Apr 7, 2010 at 5:21 PM, Yi Jiang <span dir="ltr"><<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">Dear All,</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">I computed diffusion tensors and FA,
va0 (primary eigenvalue), va1 (secondary eigenvalue), and va2 (tertiary
eigenvalue) by linear fitting in DTIStudio. Then I save them into raw matrix and
read them in matlab.</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">I found the number of non-zero (the
background is all zero) voxels for va1 and va2 is less than that of va0 or FA.
Such as:</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">number of non-zeros voxels for
va0 = 6311454<br>number of non-zeros voxels for
va1 = 6310767<br>number of non-zeros voxels for
va2 = 6248757<br>number of non-zeros voxels for
va0 = 6311454</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">This happens in all my datasets,
consistently.</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">The voxels where va0~=0 & va1==0
are not a lot (a few hundred), and they mostly are at the edge of the brain, not
inside white mattter.</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">But the voxels where va0~=0 &
va2==0 are quite a lot (tens of thousand), and they resides mostly inside white
matter, such as corpus callosum.</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">I would like to know why this
happens. </span></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;"></span> </p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">Moreover, when I try to, for
example, calculate the mean va2 within corpus callosum, how can I deal with
those voxels where va2==0 ? I think to treat them as equal to 0 sounds not
correct physiologically. But because there are a lot, I want to count those
points in, especially for small white matter structures (sometimes those va2==0
voxels can take up to 10% of a white matter structure). </span></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;"></span> </p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">Also, when I calculate radial
diffusivity (va1+va2)/2, the va2==0 points generate incorrect radial
diffusivity.</span></p>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">Thank you very
much!</span></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font size="3"><font face="Times New Roman"> </font></font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">Best,</span></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial; font-size: 10pt;">Yi</span></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font size="3"><font face="Times New Roman"> </font></font></p></font></div></div>
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