Hi there
Steve will answer your first question later..
> The other thing I can't understand is about the -ref
> option in flirt. When I do registration, the ref
> should be the target image the source image is going
> to. But when applying transform to another image,
> which should be the ref? In the "transform images and
> masks" part of siena_diff code, you used image 1
> (argv[1]) as ref. Why?
In the case of simply applying a transform to an image,
the output will have the same dimensions and voxel size as
the reference image. The actual contents of the image are ignored.
So in this case Steve wants his output to have the same dimensions
and voxel size as his image 1, so he chooses it as the reference.
> If I transform image 1 to halfway position between 1
> and 2, and then transform 1_halfwayto_2 to standard
> image. After that I apply concatenated transform to
> transform image directly to standard space, assuming
> that halfway image and standard image both have cubic
> voxels. Which image should I use as ref?
Again - If you want the output to have the same dimensions and
voxel size as the standard image, you should choose the standard image as
your reference..
Hope this helps.
Tim
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