Hi Susumu,<div><br></div><div>When I was doing my testing during the last couple weeks, I was using the VB17 software. I tried large rotations (30-45 degrees) on the sagittal orientation, and my gradient, as extracted using DTIStudio 3.0.2, was not rotated:</div>
<div><br></div><div>Using no oblique angles:</div><div><div> 0: 0.000, 0.000, 0.000</div><div> 1: 0.863, -0.364, 0.352</div><div> 2: 0.863, 0.364, 0.352</div><div> 3: 0.863, 0.364, -0.352</div><div> 4: 0.863, -0.364, -0.352</div>
<div> 5: 0.357, -0.364, -0.860</div><div> 6: 0.357, -0.866, -0.350</div><div> 7: 0.357, -0.866, 0.350</div><div> 8: 0.357, -0.364, 0.860</div><div> 9: 0.357, 0.364, 0.860</div><div> 10: 0.357, 0.866, 0.350</div><div> 11: 0.357, 0.866, -0.3509</div>
<div> 12: 0.357, 0.364, -0.860</div><div>ImageOrientationPatient: [ 1 0 0 0 1 0 ]</div><div><br></div><div>Using an oblique angle:</div><div><div> 0: 0.000, 0.000, 0.000</div><div> 1: 0.861, -0.366, 0.354</div>
<div> 2: 0.864, 0.361, 0.350</div><div> 3: 0.861, 0.366, -0.354</div><div> 4: 0.864, -0.361, -0.350</div><div> 5: 0.358, -0.352, -0.865</div><div> 6: 0.357, -0.866, -0.350</div><div> 7: 0.355, -0.861, 0.365</div><div> 8: 0.357, -0.365, 0.860</div>
<div> 9: 0.358, 0.352, 0.865</div><div> 10: 0.357, 0.866, 0.350</div><div> 11: 0.356, 0.861, -0.364</div><div> 12: 0.357, 0.365, -0.860</div></div><div>ImageOrientationPatient: [ 1.0000 0 0 0 0.8846 -0.4664 ]</div>
<div><br></div><div>However, when I tick on the "rotate gradients if applicable" button, then the oblique angle is properly taken into account. The case was the same when I used oblique angles on the axial orientation.</div>
<div><br></div><div>Although I can not do these same tests for our older software (VB13 and VA25A), just by looking at the extracted gradients, I can tell that they are not automatically rotated.</div><div><br></div><div>
I hope that helps and thank you for all of your support!</div><div>Jeff</div><div><br></div><br><div class="gmail_quote">On Tue, Dec 14, 2010 at 10:31 AM, susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Jeff,<div><br></div><div>Thank you for the follow up. Are you using VB17 and did you still need the rotation?</div>
<div><br></div><div><font color="#888888">Susumu</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Tue, Dec 14, 2010 at 3:20 PM, Jeff Sadino <span dir="ltr"><<a href="mailto:jsadino.queens@gmail.com" target="_blank">jsadino.queens@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thank you everybody! That did the trick :)<div><br></div><div>As a heads up to other people, I have heard that 3T Siemens VB17 Trio Tim is supposed to rotate the gradients automatically. I tried rotating the imaging plane by 45 degrees in both the sagittal and then the axial views to test this. On our system, the gradients were not rotated automatically. The assistance of DTIStudio is still needed in order to correct for rotated gradients in this scenario. The case is the same using the VB13 software.<br>
<div><br></div><div>Mahalo again!</div><div>Jeff Sadino<br><br><div class="gmail_quote">On Tue, Dec 14, 2010 at 8:29 AM, Meredith Reid <span dir="ltr"><<a href="mailto:mer.reid@gmail.com" target="_blank">mer.reid@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I think the last row of your rotation matrix should be the cross product of the two rows from ImageOrientationPatient, resulting in:<br>
<br><div><div><div> 1.0000 0 0</div><div><div> 0 0.8846 -0.4664</div>
</div></div><div> 0 0.4664 0.8846<br><font color="#888888"><br>Meredith<br></font></div></div><div><div></div><div><br><br><div class="gmail_quote">On Mon, Dec 13, 2010 at 5:03 PM, Jeff Sadino <span dir="ltr"><<a href="mailto:jsadino.queens@gmail.com" target="_blank">jsadino.queens@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">Hello,<div><br></div><div>Thank you Venkat and Hangyi for you insights. I tried both methods, but I was not able to replicate the values that DTIStudio gave me. The values that DTIStudio gave me, after clicking the "rotate gradients if applicable" button and for the first direction, is:</div>
<div>0.861, -0.489, 0.142</div><div><br></div><div>Here is my original gradient table:</div><div><div> 0 0 0</div><div> 0.8608 -0.3657 0.3538</div><div> 0.8643 0.3611 0.3502</div>
<div>
0.8608 0.3657 -0.3538</div><div> 0.8644 -0.3608 -0.3502</div><div> 0.3582 -0.3523 -0.8646</div><div> 0.3571 -0.8658 -0.3504</div><div> 0.3554 -0.8606 0.3648</div><div> 0.3566 -0.3652 0.8599</div>
<div> 0.3579 0.3521 0.8648</div><div> 0.3571 0.8658 0.3504</div><div> 0.3557 0.8609 -0.3638</div><div> 0.3569 0.3655 -0.8597</div><div><br></div><div>And here is my ImageOrientationPatient info:</div>
<div><div> 1.0000 0 0</div><div><div> 0 0.8846 -0.4664</div></div></div><div><br></div><div>If I do it according to Venkat, it becomes:</div><div><div> 1.0000 0 0</div>
<div><div> 0 0.8846 -0.4664</div>
</div><div> 0 0 1.0000</div></div><div><br></div><div>If I multiply my gradient by this, for the first direction, I get:</div><div> 0.8608 -0.3235 0.5244</div><div><br></div><div>If I do it according to Hangyi, the rotation matrix becomes:</div>
<div><div> 1.0000 0 0</div><div><div> 0 0.8846 -0.4664</div></div><div> 0 0.8846 -0.4664</div></div><div><br></div><div>If I multiply my gradient by this, for the first direction, I get:</div>
<div> 0.8608 -0.0106 0.0056</div><div><br></div><div>The only thing that I can think of is there is probably a step in there that normalizes the gradient to one. i.e.: sqrt(grad_x^2 + grad_y^2 + grad_z^2) = 1.</div>
<div><br></div><div>Can anybody help point me to the next step? Thank you very much!!</div><div>Jeff Sadino</div><div><div></div><div><br><div class="gmail_quote">On Fri, Dec 10, 2010 at 4:07 AM, Hangyi Jiang <span dir="ltr"><<a href="mailto:hjiang@jhmi.edu" target="_blank">hjiang@jhmi.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">hello,<br>
<br>
the 3rd row should be the outer product of the given two vectors, not [0,0,1]<br>
<br>
regards<br>
<br>
hangyi<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
________________________________<br>
From: <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] On Behalf Of Rajagopalan, Venkateswaran [<a href="mailto:rajagov2@ccf.org" target="_blank">rajagov2@ccf.org</a>]<br>
Sent: Friday, December 10, 2010 9:01 AM<br>
<div>To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
</div>Subject: Re: [Mristudio-users] Adjusting Gradients for Oblique Angles<br>
<div><div></div><div><br>
Dear Jeff Sadino,<br>
<br>
This is what I did for manual oblique angle correction<br>
<br>
multiply your gradient matrix (I don't know how many directions you have) if you have 12 directional data then you will have 3*13 (one b=0 values too) with the "Image Orientation patient" matrix<br>
<br>
[ 1 0 0 0 .8846 -.4664] rewritten as (these are unit vectors with z direction being 0 0 1 not mentioned in the Image Image orientation patient from Dicom header<br>
<br>
[ 1 0 0<br>
0 0.8846 -0.4664<br>
0 0 1]<br>
<br>
3*3<br>
<br>
Multiply the ablove Image orientation patient with your gradient matrix.<br>
<br>
Thanks<br>
<br>
Venkat<br>
<br>
________________________________<br>
From: <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> on behalf of Jeff Sadino<br>
Sent: Thu 12/9/2010 6:09 PM<br>
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
Subject: [Mristudio-users] Adjusting Gradients for Oblique Angles<br>
<br>
Hello,<br>
<br>
Thank you for the DTI training session in Turtle Bay last week. It was very helpful for us!<br>
<br>
I am wondering how to manually adjust the gradients for an oblique angle. I am using Siemens 3T Trio Tim VB17.<br>
<br>
My default gradient (for one direction) is:<br>
0.861, -0.366, 0.354<br>
<br>
After clicking "Rotate gradients if applicable" in DTIStudio 3.0.2 (March2010), the gradient is:<br>
0.861, -0.489, 0.142<br>
<br>
I couldn't find exactly which tag in the DICOM header contains the rotation information. The closest I could find is "ImageOrientationPatient". The value for this is:<br>
[ 1 0 0 0 .8846 -.4664]<br>
<br>
How do I go from the default gradient to the rotated gradient? Also, can I use this same method on the VB13 and VA25 software?<br>
<br>
Thank you very much for your help!<br>
Jeff Sadino<br>
<br>
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