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> 1.0000 0 0</div><div><div> 0 0.8846 -0.4664</div>
</div><div> 0 0.4664 0.8846<br><br>Meredith<br></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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