Hi Again,
Aligning is what registration does, so I'm not entirely sure what you want here.
If your images have been reconstructed with scanner coordinates embedding in the qform or sform component of the nifti then you can do a non-registration alignment by using the scanner coordinate systems (only useful if the placement within the scanner was very consistent) using the following call to FLIRT:
flirt -in inputimage -ref referenceimage -usesqform -applyxfm -out input2ref -omat input2ref.mat
All the best,
Mark
On 31 Jul 2012, at 04:40, Jeff Thompson wrote:
> Hello,
>
> Is there a simple method of aligning images (skull stripped or not) before registration? This would hopefully improve the results when registering the images to one another.
>
> -Thank you,
>
> Jeff Thompson
>
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