[Mristudio-users] Adjusting Gradients for Oblique Angles
Jeff Sadino
jsadino.queens at gmail.com
Tue Dec 14 16:00:25 EST 2010
Hi Susumu,
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:
Using no oblique angles:
0: 0.000, 0.000, 0.000
1: 0.863, -0.364, 0.352
2: 0.863, 0.364, 0.352
3: 0.863, 0.364, -0.352
4: 0.863, -0.364, -0.352
5: 0.357, -0.364, -0.860
6: 0.357, -0.866, -0.350
7: 0.357, -0.866, 0.350
8: 0.357, -0.364, 0.860
9: 0.357, 0.364, 0.860
10: 0.357, 0.866, 0.350
11: 0.357, 0.866, -0.3509
12: 0.357, 0.364, -0.860
ImageOrientationPatient: [ 1 0 0 0 1 0 ]
Using an oblique angle:
0: 0.000, 0.000, 0.000
1: 0.861, -0.366, 0.354
2: 0.864, 0.361, 0.350
3: 0.861, 0.366, -0.354
4: 0.864, -0.361, -0.350
5: 0.358, -0.352, -0.865
6: 0.357, -0.866, -0.350
7: 0.355, -0.861, 0.365
8: 0.357, -0.365, 0.860
9: 0.358, 0.352, 0.865
10: 0.357, 0.866, 0.350
11: 0.356, 0.861, -0.364
12: 0.357, 0.365, -0.860
ImageOrientationPatient: [ 1.0000 0 0 0 0.8846
-0.4664 ]
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.
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.
I hope that helps and thank you for all of your support!
Jeff
On Tue, Dec 14, 2010 at 10:31 AM, susumu mori <susumu at mri.jhu.edu> wrote:
> Hi Jeff,
>
> Thank you for the follow up. Are you using VB17 and did you still need the
> rotation?
>
> Susumu
>
>
> On Tue, Dec 14, 2010 at 3:20 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:
>
>> Thank you everybody! That did the trick :)
>>
>> 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.
>>
>> Mahalo again!
>> Jeff Sadino
>>
>> On Tue, Dec 14, 2010 at 8:29 AM, Meredith Reid <mer.reid at gmail.com>wrote:
>>
>>> I think the last row of your rotation matrix should be the cross product
>>> of the two rows from ImageOrientationPatient, resulting in:
>>>
>>> 1.0000 0 0
>>> 0 0.8846 -0.4664
>>> 0 0.4664 0.8846
>>>
>>> Meredith
>>>
>>>
>>> On Mon, Dec 13, 2010 at 5:03 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:
>>>
>>>> Hello,
>>>>
>>>> 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:
>>>> 0.861, -0.489, 0.142
>>>>
>>>> Here is my original gradient table:
>>>> 0 0 0
>>>> 0.8608 -0.3657 0.3538
>>>> 0.8643 0.3611 0.3502
>>>> 0.8608 0.3657 -0.3538
>>>> 0.8644 -0.3608 -0.3502
>>>> 0.3582 -0.3523 -0.8646
>>>> 0.3571 -0.8658 -0.3504
>>>> 0.3554 -0.8606 0.3648
>>>> 0.3566 -0.3652 0.8599
>>>> 0.3579 0.3521 0.8648
>>>> 0.3571 0.8658 0.3504
>>>> 0.3557 0.8609 -0.3638
>>>> 0.3569 0.3655 -0.8597
>>>>
>>>> And here is my ImageOrientationPatient info:
>>>> 1.0000 0 0
>>>> 0 0.8846 -0.4664
>>>>
>>>> If I do it according to Venkat, it becomes:
>>>> 1.0000 0 0
>>>> 0 0.8846 -0.4664
>>>> 0 0 1.0000
>>>>
>>>> If I multiply my gradient by this, for the first direction, I get:
>>>> 0.8608 -0.3235 0.5244
>>>>
>>>> If I do it according to Hangyi, the rotation matrix becomes:
>>>> 1.0000 0 0
>>>> 0 0.8846 -0.4664
>>>> 0 0.8846 -0.4664
>>>>
>>>> If I multiply my gradient by this, for the first direction, I get:
>>>> 0.8608 -0.0106 0.0056
>>>>
>>>> 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.
>>>>
>>>> Can anybody help point me to the next step? Thank you very much!!
>>>> Jeff Sadino
>>>>
>>>> On Fri, Dec 10, 2010 at 4:07 AM, Hangyi Jiang <hjiang at jhmi.edu> wrote:
>>>>
>>>>> hello,
>>>>>
>>>>> the 3rd row should be the outer product of the given two vectors, not
>>>>> [0,0,1]
>>>>>
>>>>> regards
>>>>>
>>>>> hangyi
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ________________________________
>>>>> From: mristudio-users-bounces at mristudio.org [
>>>>> mristudio-users-bounces at mristudio.org] On Behalf Of Rajagopalan,
>>>>> Venkateswaran [rajagov2 at ccf.org]
>>>>> Sent: Friday, December 10, 2010 9:01 AM
>>>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>>>>> Subject: Re: [Mristudio-users] Adjusting Gradients for Oblique Angles
>>>>>
>>>>> Dear Jeff Sadino,
>>>>>
>>>>> This is what I did for manual oblique angle correction
>>>>>
>>>>> 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
>>>>>
>>>>> [ 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
>>>>>
>>>>> [ 1 0 0
>>>>> 0 0.8846 -0.4664
>>>>> 0 0 1]
>>>>>
>>>>> 3*3
>>>>>
>>>>> Multiply the ablove Image orientation patient with your gradient
>>>>> matrix.
>>>>>
>>>>> Thanks
>>>>>
>>>>> Venkat
>>>>>
>>>>> ________________________________
>>>>> From: mristudio-users-bounces at mristudio.org on behalf of Jeff Sadino
>>>>> Sent: Thu 12/9/2010 6:09 PM
>>>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>>>>> Subject: [Mristudio-users] Adjusting Gradients for Oblique Angles
>>>>>
>>>>> Hello,
>>>>>
>>>>> Thank you for the DTI training session in Turtle Bay last week. It was
>>>>> very helpful for us!
>>>>>
>>>>> I am wondering how to manually adjust the gradients for an oblique
>>>>> angle. I am using Siemens 3T Trio Tim VB17.
>>>>>
>>>>> My default gradient (for one direction) is:
>>>>> 0.861, -0.366, 0.354
>>>>>
>>>>> After clicking "Rotate gradients if applicable" in DTIStudio 3.0.2
>>>>> (March2010), the gradient is:
>>>>> 0.861, -0.489, 0.142
>>>>>
>>>>> 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:
>>>>> [ 1 0 0 0 .8846 -.4664]
>>>>>
>>>>> 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?
>>>>>
>>>>> Thank you very much for your help!
>>>>> Jeff Sadino
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
>>>>
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