Hi,
Flirt does not use the sform or qform information for registration by
default.
It does use (and relies upon) the voxel sizes in mm.
If you turn on the -usesqform option then it will initialise the
registration
with the sform or qform information, but *only* if one of the qform or
sform
codes is non-zero (otherwise they are both considered "unknown" and
they are ignored).
So if you see no difference when using -usesqform then I would imagine
that
either the codes are both zero (in either image) or that the initial
alignment
imposed by this is sufficiently similar to the default, or one of the
many initial
starting positions that flirt tries at the start of the optimisation,
that it leads to
the same solution. This would make sense if the registration was
succeeding.
Is the registration working well?
All the best,
Mark
On 15 May 2009, at 09:25, Erlend Hodneland wrote:
> I am trying to to multimodal registration using flirt. When I open
> the input
> nifti files I see they have header information for the real space
> coordinates inside the "sform" field. My questions are as following:
>
> 1. Is flirt using any header information for registration? To me, it
> seems
> so, since I get different results if I run flirt the same .nii image
> with
> and without the header.
>
> 2. If header information is used, why are the results not improved
> when I
> use the option "-usesqform" in flirt, compared to the situation
> without this
> option?
>
> Best regards
>
> Erlend Hodneland
>
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