Hi,
Thank you very much for you reply!
My "sform_code = 1" in both the refence image and the input image.
My registration results are not good, even if I use "-usesqform" or not. The
results are similar, but dont look good.
My wish is to make flirt use ONLY the sform information, and not performing
any optimization. I tried this by setting "-nosearch" in addition to
"-usesqform" but the results are still not good, as I obtain in Matlab with
my own code.
Do you have any suggestions?
Erlend
On Fri, 15 May 2009 09:30:30 +0100, Mark Jenkinson <[log in to unmask]> wrote:
>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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