Hi,
The registration tools will register (i.e. calculate the alignment between) two 3D images. If you feed in 4D images they will just take the first 3D volume. You can _apply_ a transformation to a 4D image, but calculating the alignment is done between 3D images only. Registering all 3D images within a 4D image to a consistent reference is a separate task - motion correction. If you want to do both, then do motion correction within each 4D image, then take the reference 3D volume from each and register these images together, then you can apply that transform to the motion-corrected 4D images to get everything aligned.
If you want to avoid a second interpolation step then you can combine the motion correction matrices and the between 4D transformations together and do the resampling in one step.
I hope this helps.
All the best,
Mark
> On 25 Apr 2017, at 14:59, Usman Sheikh <[log in to unmask]> wrote:
>
> Sorry, I was a so quick in pressing the "send" button that I didn't even mention the actual problem.
>
> So, I am trying to align all three volumes, one by one, using Flirt GUI. I am inputting first filtered_func 4D image as a reference and second/third/fourth filtered_func image as input-image. Now what I am expecting to get, as an output image, is a 4D aligned image but what I am getting actually is just a 500 KB file including one 3D image.
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