[Mristudio-users] Questions about frames

[Xu Li]

Thanks a lot for clarifying.

One follow up question is how can we transfer them back to the lab frame, which we are interested in for our project. Is there a way we can get the transfer matrix? Or when we transfer from lab frame to the image frame, does the DTI_studio use the rotation order like T = T_RL*T_AP*T_FH? Supposing the T_FH is the rotation matrix defined by the FH angulation in the scanner and etc.

Thanks!

Xu


On Oct 27, 2010, at 11:02 AM, susumu mori wrote:

> Lab frame may be used in data acquisition, but in the image analysis world, everything has to be in the image frame. If you don't use oblique imaging, these two frames are the same (aligned). So, you don't have to worry about it. The only freedom left is permutation. For example, [0 0 1] in lab frame (Z gradient), could be image X, Y, or Z, depending on your slice orientations (coronal -> Y, sagittal -> Y, axial -> Z).
> 
> If you use oblique imaging, lab frame [0 0 1] could be image frame [0, 0.25, 0.97] if the image is 15 degree rotated. In image analysis, you want to use [0, 0.25, 0.97] and usually forget about [0 0 1] because you don't retain the information "15 degree" in image analysis. As long as you throw away (we usually throw away) this "15 degree" information, the image frame you are working on is dissociated from the lab frame. In the end, what you are interested in is brain anatomy, not the absolute orientation of the lab frame, which we don't care.
> 
> On Wed, Oct 27, 2010 at 10:44 AM, Xu Li <xuli at mri.jhu.edu> wrote:
> Dear Susumu and Hangyi,
> 
> I have one quick questions about the eigenvectors we can get from DTI-Studio. Are they defined in the image frame or the lab frame? I understand that the gradient is applied according to the image frame but the correct gradient table should be defined in lab frame (i.e. if we acquire 0 angulation data, the very first gradient vector would be [0 0 1] or some thing like that).  But after we do the tensor fitting and eigenvalue decomposition, are they still in lab frame? I guess it is, but just want to confirm.
> 
> Thanks!
> 
> Xu
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