[Mristudio-users] NifTi and DTI Studio

[susumu mori]

>
>
>
> Thanks for this information i also thought about this, but one question
> prevented me from doing this, i would like to clarify that with you, after
> distortion correction especially the voxels in frontal regions of the brain
> like corpus callosum ( i am not good in anatomy sorry apologize me if i am
> wrong) are streched or in other words restored to their original positions,
> so i am wondering whether this kind of voxel stretching and squeezing
> (undistorted) will contribute to any additional changes in b-matrix when
> compared to the changes in b-mtarix contributed by the original i.e
> distorted images. I understand that b-matrix rotation i calculated from the
> rotation matrix of the main affine matrix, i don't know whether the affine
> matrix will be different between before and after distortion correction
> images. I am sorry if i am not clear.
>
>
>
This is a good point. In a short answer, I believe that you don't have to
worry about b-table or tensor reorientation for B0 distortion correction.
Here is why;

> For DWI, we first apply diffusion weighting along one axis, for example,
along X axis (b = [1, 0, 0]). Then we apply imaging gradient to obtain an
image; a circle object should look circle. During the data acquisition, B0
susceptibility influences the acquisition and brain signal intensity is
"mislocated"; the circle object may look oval now.Important thing is, the
diffusion weighting scheme and the imaging scheme are two separate
process. B0 correction simply correct this mis-registered signal to the
right place; the oval is corrected to a circle. For example, suppose you
have two pixels side-by-side and a fiber is running along the right-left
connecting the two pixels. If you apply [1, 0, 0] gradient (=x axis), both
pixels look dark. If gradient is [0, 1, 0], they look bright. Tensor
calculation tells that the fibers are running horizontally connecting the
two pixels. Then if B0 distortion misplaces the right pixel shifted upward
and now they are located at 45 degree each other. The tensor calculation
still tells that the fiber is running holizontally. In this case, we want to
move the right pixel shifted downward without touching the tensor
calculation; now they are side-by-side and connected by the fiber. If you
apply b-table rotation or tensor re-orientation, by the time the two pixels
are aligned side-by-side, the fiber angles are rotated 45 degree running
diagonally, which you don't want. I hope this makes sense.

> When you are dealing with mis-registration by patient motion, it is a very
different story. Suppose we run two DTI set. In the first set, the brain is
upright when [1,0,0] gradient is applied and in the second set, the brain is
5 degree tilted and the same [1, 0, 0] is applied. Then we co-register these
two images by rotating the second set by -5 degree. In this case, you have
to rotate the second [1, 0, 0] b weighting by -5 degree to keep the
consistency between the two sets. I think this is understandable.

> Like wise, if you are trying to normalize two brains; say one is circle
and the other is oval. In this case, when pixels are shifted to make the
oval to the circle, you have to re-orient the b-table

> When an object shape is transformed, you can either reorient the b-table
before the tensor calculation or do the tensor calculation first and then
rotate the tensor. They may provide slightly different results. Therefore,
you'd better pick one of the methods and stick to it.

I hope this helps.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090901/dc9ae589/attachment-0001.html