[Mristudio-users] extraction of Tensor values

[Thomas Ballinger]

I don't know much about DTI studio, but I recently had to do this, and I did
it by extracting the diffusion tensor scalar directions (saving the xx xy xz
yy yz zz directions) as separate volumes.  I saved them as NRRD volumes
because that was what I needed, but analyze format was also an option.
There are several Matlab libraries for loading nifti files, though I don't
know much about them.  I bet other folks will have better suggestions.

Thomas Ballinger

On Mon, Jan 31, 2011 at 8:36 AM, Syed Salman Shahid <
SyedSalman.Shahid at usq.edu.au> wrote:

>  Hi,
>
>
>
> 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?
>
>
>
> With regards
>
> Salman
>
>
>
>
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu mori
> *Sent:* Sunday, 30 January 2011 8:57 AM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] question - changes of FA and eigenvalues
> after Gd contrast
>
>
>
> Hi Amir, nice observation.
>
>
>
> 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.
>
>
>
> 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.
>
>
>
> 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.
>
>
>
> 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.
>
>
>
>
>
>
>
> On Sat, Jan 29, 2011 at 12:43 PM, Amir Zolal <amirzolal at gmail.com> wrote:
>
> Hi,
>
> I have tried comparing DTI images before and after Gd contrast
> administration, and I have found that the FA was increased after the
> contrast agent (more in the ROIs where there was contrast
> enhancement), I have also (among other things) seen a significant
> decrease of all eigenvalues, however the third eigenvalue decreased
> the most (the difference between the change of lambda1 and lambda3 was
> also significant), causing the paradoxical increase in FA. This was
> not observable in the normal white matter. Because I don't believe,
> that the contrast agent would in any way influence water diffusion, my
> theory is, that the addition of a paramagnetic contrast agent  could
> cause more local noise and the small attenuation in the (lambda3)
> direction would be even less discernible, in contrast to the strong
> attenuation in the (lambda1) direction. My question is, to your
> knowledge, would there be anything else in the processing of the DTI
> datasets that could cause the above described effect?
>
> Thanks in advance for your ideas,
>
> Amir
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