[Mristudio-users] Scanner-specific gradients?

[susumu]

Hi Igor,

Unless you explicity change the gradient table, the same imaging protocol
should use the same gradient table.
However, there are several things that make the matter complicated;

1) The manufacturers provide gradient tables. For example, Siemens has 6-
and 12-orientation tables. While they provide only one kind of the
12-orientation Siemens table, when actual scan happens, they dynamically
change the table.
2) For example, you may use axial, coronal, or sagital scans. The patient
may go in the scanner head-first or leg-first. Or they could be face up,
face down, or facing to the side. There are so many possibilities related to
the relative relationship between the subject, the physical gradients, and
the imaging parameters. Apparently, one gradient table can not be applied to
all these setttings. 
3) One of the issues due to this type of degrees of freedom is that the +/-
sign of the gradient table may not represent what the scanner actually did.
As a matter of fact, the +/- sign is arbitrary defined. What is most
important is the relationship between the diffusion gradients and imaging
gradients, which are changed dynamically depending on your protocol.
Usually, for siemens, axial, head-first, face-up, the sign of the X gradient
has to be flipped.
4) If you look the two tables you got carefully, you notice that the x
components have opposite signs. I suspect the first one is the one provided
by Siemens and the second one is read from DICOM header. The latter one
reflects what was actually done by the scanner, I believe.
5) If you use the one provided by the manufacturer (the first one) for
tensor calculation, it won't affect your FA, ADC, and diffusivity, but it
affects vector angles (and thus fiber tracking). This is why DtiStudio has a
function of "flip" before fiber tracking. Of course, it is much better
approach to use the second table with the correct +/- sign.
5) The second thing you notice is that there is a small differences in each
component. I suspect this is because you used oblique imaging. Please check
if this is actually the case. This is a very tricky issue and you have to
make sure that you are doing a right thing. Not using oblique makes
situation much simpler, but if you want to use oblique, you have to consider
the following;
6) If you are using older operating system of Siemens, you HAVE TO
recalculate your gradient table based on oblique angles. You can do it
automatically if you are using DICOM or Mosaic. You have to check "rotate
gradient if applicable" box. Then DtiStudio read the oblique information and
reorient the table for you.
7) If you are using the latest operating system, you don't have to
recalculate the table. So you don't want to check the "rotate gradient if
appliable" box. Either way, it is advised to image one person with a severe
oblique plane, process the data, and perform tracking. This immediately
tells if things are correctly working. Vendors change things without notice.
You'd better learn how to protect yourself. 
8) If you are not sure, you can send the tracking results to us.

Susumu 





-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Yakushev
Sent: Thursday, February 26, 2009 12:13 PM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: [Mristudio-users] Scanner-specific gradients?

Dear Susumu, dear Users,
I have a beginners question:Should be the combination of gradients the same
for all subjects imaged with the same scanner (i.e. scanner-specific
gradients)? Or the gradients may be different for different scans/subjects
(i.e. scan-specific gradients)? Such "individual" gradients (bvec) can be
calculated using e.g. MRIcron.
For example, gradient table (as provided by radiologists) in the first case
looks like:
0: 0, 0, 0 1: -0.7, 0, -0.7 2: 0.7, 0, -0.7 3: 0, 0.7, -0.7 4: 0, 0.7, 0.7
5: -0.7, 0.7, 0 6: 0.7, 0.7, 0 in the second case (calculated with MRIcron)
completely different:
0: 0.000, 0.000, 0.000 1: 0.704, -0.146, -0.695 2: -0.710, -0.146, -0.689 3:
0.004, 0.546, -0.838 4: 0.003, 0.838, 0.546 5: 0.706, 0.692, -0.149 6:
-0.708, 0.692, -0.142 Accordingly, results (tracks originated from the same
ROI) are very different.
Thanks,Igor_______________________________________________Mristudio-users
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