[Mristudio-users] extraction of Tensor values

[Syed Salman Shahid]

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<mailto: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
_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<mailto:mristudio-users-unsubscribe at mristudio.org>


This email (including any attached files) is confidential and is for the
intended recipient(s) only.  If you received this email by mistake,
please, as a courtesy, tell the sender, then delete this email.

The views and opinions are the originator's and do not necessarily
reflect those of the University of Southern Queensland.  Although all
reasonable precautions were taken to ensure that this email contained no
viruses at the time it was sent we accept no liability for any losses
arising from its receipt.

The University of Southern Queensland is a registered provider of
education with the Australian Government (CRICOS Institution Code No's.
QLD 00244B / NSW 02225M)


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20110131/66830301/attachment-0001.html