Hi all,<div><br></div><div>Because the gradient rotation is a very tricky issue, I want to revisit it.</div><div><br></div><div>1) First of all, this is a complicated issue. Manufacturer may change the way they perform diffusion weighting and store the information during upgrade. So, as I mentioned before, you need to do several testings by yourself. It is very difficult to provide a tool that is guaranteed to work in all situations.</div>
<div><br></div><div>2) You don't have to worry about this issue if you are not using oblique imaging, meaning you always use simple sagittal/coronal/axial scans without FOV (field of view) rotations.</div><div><br></div>
<div>3) When FOV is rotated (e.g. AC-PC alignment or to compensate brain tilt), there are two potential options. Suppose a DWI is acquired with [1, 0, 0] (diffusion along X ). In the first option, after the FOV rotation (say, 5 degree about Z axis), [1, 0, 0] remains "physical" X gradient. So, oblique rotation has no impact on the gradient application. In the second option, [1, 0, 0] means diffusion weighting along FOV (image matrix) X axis, which is no longer the same as the physical gradient X axis. In this case, the actual diffusion-weighting is [cos(5), sin(5), 0]. Namely, the diffusion table rotates with the FOV.</div>
<div><br></div><div>4) As fur as I know, Philips and GE currently do the latter ([cos(5), sin(5), 0]) and Siemens does the former ([1, 0, 0]). However, for Philips, if an option called "GradientOverplus" is ON, it does the former ([1, 0, 0]).</div>
<div><br></div><div>5) If your scanner does the dynamic diffusion table rotation, following the FOV rotation, you do NOT want to click the "rotate table" option. This means, Philips and GE data usually do not have to rotate table.</div>
<div><br></div><div>6) If your scanner doesn't do the table rotation ([1,0,0] remains physical [1, 0, 0] regardless of the FOV rotation), you NEED to click the "rotate table" option. This means, we usually choose this option if you are using Siemens.</div>
<div><br></div><div>7) I am not sure what would happen if you use "user-defined" options in these scanners. Also, the way the gradient table information is stored in the header files (does "X" means physical gradient X or image matrix X) may not be consistent among manufacturers as well as different files types with in the same manufacturer (e.g. DICOM and PAR/REC formats of Philips). </div>
<div><br></div><div>7) I want to stress that it is very difficult for us to give you the correct answers because there are so many variables and potential changes after scanner upgrades. Therefore, we always suggest you to do small tests.</div>
<div><br></div><div>Test</div><div>A> obtain one set of DTI. Usually you don't see noticeable difference between "rotate gradient" ON/OFF</div><div>B> Then obtain another set of DTI with a severe oblique angle (like 30 degrees). The brain looks rotated. Now you see difference between "rotate gradient" ON/OFF</div>
<div>C> (optional) you can ask the subject to rotate the head significantly (like 30 degrees) and rotate the FOV to make the brain looks upright in the image. Again, you should see difference between "rotate gradient" ON/OFF.</div>
<div><br></div><div>If you are processing your data correctly,</div><div>The color map of B should look very different from A. </div><div>C should give you a color map similar to A.</div>
<div><br></div><div>In all cases, tractography should work and produce similar results.</div><div>If A color map has similar appearance as B color map, or C color map doesn't look like A color map, then your DTI calculation is not working. Please check if it can be solved by checking or unchecking the "rotate gradient" option.</div>
<div><br></div><div>I would appreciate users to share your findings or report any errors in my statement. We have an access to only a limited number of scanners and it is difficult to test different scanners.</div><div><br>
</div><div>Susumu</div><div><br><br><div class="gmail_quote">On Fri, Feb 22, 2013 at 9:16 PM, Durai Arasan <span dir="ltr"><<a href="mailto:durai23@gmail.com" target="_blank">durai23@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">and this <div><br></div><div><a href="http://lists.mristudio.org/pipermail/mristudio-users/2010/001359.html" target="_blank">http://lists.mristudio.org/pipermail/mristudio-users/2010/001359.html</a><div>
<div><br><br><div class="gmail_quote">On Fri, Feb 22, 2013 at 9:13 PM, Durai Arasan <span dir="ltr"><<a href="mailto:durai23@gmail.com" target="_blank">durai23@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>this might help</div><div><br></div><a href="http://lists.mristudio.org/pipermail/mristudio-users/2010/001868.html" target="_blank">http://lists.mristudio.org/pipermail/mristudio-users/2010/001868.html</a><br>
<br><div class="gmail_quote"><div><div>
On Fri, Feb 22, 2013 at 11:28 AM, Vanessa Douet <span dir="ltr"><<a href="mailto:douet@hawaii.edu" target="_blank">douet@hawaii.edu</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div>
Hi,<br><br>I am a very new user of the MRI studio. I am learning how to use your software. Could you explain to me when and why the "rotate gradient if applicable" has to be checked ?<br><br>Thank you very much<span><font color="#888888"><br>
<br>Vanessa<br clear="all"><br>-- <br>Vanessa Douet, <span>PhD</span><br>Department of Medicine<br>John A. Burns School of Medicine<br>The Queen's Medical Center<br>1356 Lusitana Street, UH Tower, 7th floor<br>Honolulu, HI 96813<br>
<a value="+18085867467">(808) 586-7468</a>
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