[Mristudio-users] gradient directions

[Jeff Sadino]

Hi Darren,

I also spent some time on this recently on our Siemens VB17 software.
 DTIStudio does not rotate the gradients until after you click "OK" to
visualize your images.  So regardless of whether or not you select "rotate
gradients if applicable", the gradient table that you will see DTIStudio
pull will be identical.  To see the modified table, visualize your data,
then close that window, then when you load up your next subject, you will
see the rotated table.

As far as I can tell, DTIStudio pulls whatever is written in the DICOM
header, without any modifications, unless you tell it to.

In the DICOM header, there is a tag called ImageOrientationPatient.
 DTIStudio uses this tag to "know" whether or not a rotation is necessary.

I'm not sure about those specific third party programs, but I think some of
them flip the y direction so that they are more compatible with FSL

Hope it helps,
Jeff

On Sun, Dec 26, 2010 at 3:18 PM, Darren Gitelman <
d-gitelman at northwestern.edu> wrote:

> Hi
>
> I know the issue of gradient directions has been brought up many
> times, but I am struggling with what the correct gradient directions
> should be. It's not that I doubt dtistudio, but I am puzzled by why
> the gradients end up different depending on how one converts the dicom
> data. I have spent some time plotting the gradient directions on a
> unit sphere and this is what i found (see below). I also have some
> questions about how dtistudio "knows" whether or not to rotate the
> gradients.
>
> I am using Siemens data acquired on a scanner with b17 software.
>
> If I click "get gradient from dicom file header" the values entered by
> DTIstudio don't seem to change whether or not I also click rotate
> gradients if applicable.
>
> Is DTIstudio automatically rotating the gradients when it gets them
> from the Siemens header?
>
> Clearly these gradients are different than if I pasted in the default
> Siemens gradients. How does DTIstudio know whether or not the
> gradients need rotating when I click the OK button? Here is what I
> mean- let's say I get the gradients from the Dicom image and I save
> these in a text file. Now I try 2 different ways of importing the DTI
> data: 1) in one case I paste the default Siemens gradients and in the
> other 2) I paste the gradients I obtained from the Dicom image. If I
> click rotate gradients if applicable, will DTIstudio know to rotate
> the gradients in case 1 (default Siemens directions) but not in case 2
> (acquired from Dicom file)?
>
> Is there any way to get the final gradients that DTIstudio is applying
> to the data?
>
> The whole process of obtaining the gradients seems to be somewhat of a
> mystery (to me anyway) and it's hard to know what is correct (at least
> for Siemens data). I also notice that the gradients obtained from the
> Dicom file are not the same as the gradients one obtains when
> converting the data via either dcm2nii
> (http://www.cabiatl.com/mricro/mricron/dcm2nii.html) or via mriconvert
> (http://lcni.uoregon.edu/~jolinda/MRIConvert/). The gradients from
> these conversions are flipped by -1 in the y direction from dtistudio.
> (In fact the gradients from mriconvert are nearly the same as
> dtistudio after accounting for this y-flip, while the gradients form
> dcm2nii are off by 4-6 degrees rotation after accounting for the
> y-flip).
>
> Any advice about the gradient directions and how to be sure what is
> correct would be appreciated.
>
> Thanks,
> Darren
> --
> Darren Gitelman, MD
> 710 N. Lake Shore Dr., 1122
> Chicago, IL 60611
> Ph: (312) 908-8614
> Fax: (312) 908-5073
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