[Mristudio-users] Scanner-specific gradients?

Thu Mar 5 11:56:53 EST 2009

Hi Igor,

It depend on the precision of your measurement. With typical 1.5T, 2.5 mm
resolution, and 5-10 min scan, the SNR is such that we have about +/- 4
degree of measurement variability (see Fig. 8 of the attached manuscript).
In this case, it doesn't matter if you specify the gradient table with the
accuracy of 0.1 degree. I'm not sure how this is translated into the decimal
points (I think it's not difficult to calculate the actual angle difference
by rounding the numbers), but would be surprised if you need the 4th digit.

Susumu

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Yakushev
Sent: Thursday, March 05, 2009 7:45 AM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: Re: [Mristudio-users] Scanner-specific gradients?

Dear Susumu,

Thanks again for your careful answer!
We have ascertained that the scan-specific (extracted from individual 
DICOM headers) gradients were the right ones. I have one more practical 
question:

Our individual gradients have values of 14-15 digits following zero, 
e.g. -0.145791634917259.
To what decimal digit should/may one round these values? It's important 
to know, as we're going to analyse large amount of data and, as i wrote,
we have to introduce a different gradient table for each individual 
case. Of note, there is a rather small difference between the values, 
please see an example of a gradient table in my previous mail and one 
more below (rounded to 3 decimal digits):

 0: 0.000, 0.000, 0.000
 1: 0.696, -0.157, -0.701
 2: -0.718, -0.157, -0.678
 3: -0.014, 0.533, -0.846
 4: 0.009, 0.846, 0.533
 5: 0.704, 0.690, -0.168
 6: -0.710, 0.690, -0.145

Thank you!
Igor

* susumu <susumu at mri.jhu.edu> [Thu, 26 Feb 2009 20:04:51 -0500]:
> 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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