Hi,
All the sch2D_* files control the number of degrees of freedom
used for the registration. The -2D flag specifies that it should
use the sch2D_3dof degrees of freedom *and* to expect a
single slice, and appropriately pad in the through-slice direction
(for internal code reasons).
The last dof in the 6dof case is a x-y shear (or skew).
You can run any of the 2D schedule files with 3D data. It simply
applies the 2D transformation to all slices. You can use any of
the schedule files with 3D data, without using the -2D option.
It should work fine. I'm not quite sure what exactly you are
saying went wrong, but try it without the -2D option (but still
with the -schedule) and see if that works OK. Make sure you
have a 3D volume for both input and reference though, as
otherwise it won't work correctly.
All the best,
Mark
On 27 Nov 2009, at 06:29, Junqian Gordon Xu wrote:
> I want to make sure my understanding of the flirt 2D registration
> correct.
>
> ${FSLDIR}/etc/flirtsch
>
> 1) sch2D_3dof (same as -2D): x, y translation + in-plane roation
>
> 2) sch2D_5dof: sch2D_3dof + x, y scaling?
>
> 3) sch2D_6dof: sch2D_5dof + ?
>
> 4) Although the example on line suggests flirt -2D for a single
> slice, it apparently worked with 3D volume images as well in my
> trial. The obvious problem is that it only outputs ONE, instead of
> slice#, transformation matrix, which made me worried about whether I
> am abusing flirt -2D. However the resulting image did show
> improvement in alignment and did suggest the code operated on
> individual slice. Yet, can somebody know the details about flirt -2D
> verify its behavior in such situation?
>
> Thanks
> Junqian "Gordon" Xu
> National Multiple Sclerosis Society Postdoctoral Fellow
> Department of Neurology
> Washington University in St. Louis
>
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