[Mristudio-users] Adjusting Gradients for Oblique Angles
susumu mori
susumu at mri.jhu.edu
Tue Dec 14 15:31:15 EST 2010
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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>>
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