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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I would like to extract the numerical values of diffusion tensor
from the tensor.dat file using matlab. I got the Tensor.dat file from
DTIStudio, however, the format is not compatible with either notepad or matlab
importing tools. Is it possible to save this tensor file in some other text
file format?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>With regards<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Salman<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b>On Behalf Of </b>susumu mori<br>
<b>Sent:</b> Sunday, 30 January 2011 8:57 AM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] question - changes of FA and eigenvalues
after Gd contrast<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Amir, nice observation.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>For NMR/MRI of living organs, we are dealing with a system
with a huge number of compartments. Waters inside cytoplasm, nucleus, golgi,
mito, extracelluar space, bound to macromolecules, inside an axonal process,
trapped between neurofilaments/microtubles, inside myeline, etc. These
microscopic environment varies within a scale of micrometer scale or less.
Then, there are larger scale structure units such as neurons, astrocytes, then
even larger such as WM and GM, from small (tens of microns) to large (millimeter).
These structural units with different scales coexist within one pixel.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>In this complicated multi-compartment systems, water
molecules move around about 10 micron, in average, experiencing different
environments, some place could be isotropic and some could be anisotropic. If
we can assume that during the 40-60ms of observation time (typical separation
between two gradient pulses, in which water moved 10micron), all water
molecules experience all compartments and effectively averaged out the existence
of different diffusion environments, we can assume that the system is
homogeneous (fast-exchange regime). Usually, we can's assume it; many
water molecules are trapped in one compartment or visiting only several
compartments. Then our pixels consist of multiple compartments with different
diffusion environment. <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Now, it is not only diffusion properties that are different
among these compartment. Their relaxation properties are also very different.
Suppose one simple and extreme case in which we have only two compartments and
there is no exchange between them (like intra and extra-cellular spaces with
very slow membrane exchange). Also assume that intra cellular component is
dominant (90%) with high anisotropy and short T2 and extra cellular component is
minority (10%) with low anisotropy and long T2 (I just made up all these
numbers). If we use a short echo sequence, the signal from the intracelluar
compartment dominate the signal and the system looks very anisotropy. If we use
a long echo sequence, the signal from the extracellular space becomes dominant
and the same pixel now looks less anisotropic. <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>So, as long as we are dealing with multiple compartment
systems with slow exchange regime, changing relaxation time (like
altering T1 and T2) and sequence (like long echo or
rapid repetition), you can effectively change the final contribution of of
each compartment to the signal. Therefore, it is likely that T1, T2, AND
"measured" diffusion properties change by adding Gd, even if Gd doesn't
directly change water diffusion.<o:p></o:p></p>
</div>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>On Sat, Jan 29, 2011 at 12:43 PM, Amir Zolal <<a
href="mailto:amirzolal@gmail.com">amirzolal@gmail.com</a>> wrote:<o:p></o:p></p>
<p class=MsoNormal>Hi,<br>
<br>
I have tried comparing DTI images before and after Gd contrast<br>
administration, and I have found that the FA was increased after the<br>
contrast agent (more in the ROIs where there was contrast<br>
enhancement), I have also (among other things) seen a significant<br>
decrease of all eigenvalues, however the third eigenvalue decreased<br>
the most (the difference between the change of lambda1 and lambda3 was<br>
also significant), causing the paradoxical increase in FA. This was<br>
not observable in the normal white matter. Because I don't believe,<br>
that the contrast agent would in any way influence water diffusion, my<br>
theory is, that the addition of a paramagnetic contrast agent could<br>
cause more local noise and the small attenuation in the (lambda3)<br>
direction would be even less discernible, in contrast to the strong<br>
attenuation in the (lambda1) direction. My question is, to your<br>
knowledge, would there be anything else in the processing of the DTI<br>
datasets that could cause the above described effect?<br>
<br>
Thanks in advance for your ideas,<br>
<br>
Amir<br>
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