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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