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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