Dear Ben,
The direction refers to the voxel axes only.
Nothing else is taken into consideration.
In the example you use it would be necessary to use -d 2
to get the desired result.
It is not always the case that acquired slices are axial,
so there is no default besides the z axis of the acquired
voxels, as very often this is the actual slice direction for
scans that have come straight off the scanner without
any reorientation.
All the best,
Mark
On 15 Aug 2011, at 21:25, Benjamin Matthew Deen wrote:
> Hi,
>
> I have a quick question about the slice direction (-d) option of slicetimer. Does this refer to the axis in voxel space, or in physical ("RAS") space (after applying the q-form transformation)? In other words, if I have an image in, say, LSA orientation with slices acquired along the inferior-superior axis (physical z-dimension, but second dimension of voxel coordinates), will slicetimer use the correct, inferior-superior axis by default? Thanks,
>
> Ben
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