Dear Daniel,
just to chip in on Mark’s reply. It is absolutely right that fnirt is not written for and cannot do 2D warping. _But_ when we have had to do that we have been able to stack a bunch of 2D images and the do a “3D” warp, where any z-component can subsequently be ignored. To be safe I would go for a stack of at least 9 images though.
Jesper
> On 23 Aug 2018, at 10:48, Mark Jenkinson <[log in to unmask]> wrote:
>
> Hi,
>
> I'm not entirely sure whether the 3D interpolations might be a problem here (Jesper might be able to chip in if he's around). Otherwise there is a work-around for this. Just make a "3D image" that is a stacked version of your 2D image (something like 5 copies of the 2D image stacked in the z-direction) and do this for both the input and reference and then run FNIRT. This will give it no useful information in the z-direction, and so it should do a 2D warp, and then you can extract the middle slice as your output image. You can also take the warpfield and make it 2D by forcing the third volume of the warpfield to be zeros. Use fslmerge to stack things in 3D and fslsplit or fslroi to break them apart.
>
> I hope this helps.
> All the best,
> Mark
>
>
>> On 21 Aug 2018, at 16:46, Daniel Hahne <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> is it possible to use FNIRT for the registration of 2D images?
>> I tried it with the default settings but the input and output image look the same.
>>
>> Thanks for your help,
>> Daniel
>>
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