[Mristudio-users] gradient directions

[Darren Gitelman]

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