Dear Zoltan,
for my toolbox and visualisation code, gradient/tensor/eigenvector
components are assumed to be in "world space". Thus, for SIEMENS scanners
you can just have any slice orientation and use the scanner provided
gradient directions. You have to take care however if you rotate your DWI
images with SPM (e.g. through coregistration or realignment) to adjust the
gradient directions. There is a routine in the toolbox for this - it is
called "Reorient Gradients".
Volkmar
On Mon, 10 Oct 2005, Zoltan Nagy wrote:
> if you do not use slice orientations along one of the axes in scanner
> coordinates (i.e. if you use oblique slices) then you may also need to
> rotate your diffusion vectors along with your oblique slices - i am not
> sure maybe volkmar's toolbox already takes care of it. for example:
> suppose you acquire your slices rotated to the left. then a diffusion
> vector pointing along the z direction in the scanner coordinates (0,0,1)
> will not point perpendicular to the slices.
>
> this matters if you want to display color-coded images or for fiber
> tracking. although the diffusion directions are still not rotated to the
> anatomy. so when you say left-right you can only refer to the image and
> not the person's head.
>
> zoltan
>
> p.s. as far as i know, GE rotates its diffusion gradients with the
> acquired slices, philips sometimes rotates them and sometimes not and
> siemens does not rotate them.
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg
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