Hi - when you have slice gaps this should simply reflected in the
voxel dimension in the header, which should be the summation of the
slice size plus the gap - i.e., should be the distance from the start
of one slice to the start of the next. You should not insert gappy-
data-slices into the actual image.
A separate point is that in general you should use the higher-quality
image as the reference image, and if necessary then invert the
resulting transformation before applying that.
Cheers.
On 18 Mar 2009, at 16:15, Rajagopalan, Venkateswaran wrote:
> Dear FSL users,
>
> I want to register two images for instance my Reference image
> is :Image_1 and input image is Image_2 both acquired with same in
> plane resolution of 0.98*0.98*4mm but in the case of reference image
> i.e.Image_1 the FOV was chosen to cover only a part of head,so i
> have only few slices with slice gaps of 4mm thickness introduced in
> this acquisition, whereas Image_2 on the other hand was acquired
> contiguously without any slice gap covering the entire head. I want
> to register my Image_2 to Image_1 space, so my question is can i
> directly feed them into FLIRT and FLIRT will take care of this slice
> gap problem during registration or for instance do i need to insert
> zero padded images for the missing slices in my Image_1 and do the
> registration.
>
> Thanks in advance,
>
> Regards
> venkateswaran
>
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Stephen M. Smith, Professor of Biomedical Engineering
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FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
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