I'm using Flirt to align a low resolution EPI image --> high resolution
anatomical --> standard brain (avg152_brain)
all three of these images have a different field of view. When Flirt
resamples images, the default is to use the FOV of the reference image.
In my case, I want to retain the FOV of the EPI(64X64X24, 3.75X3.75X3.75).
There is an option for Flirt to use a different reference image for
reslicing, but if this image has a larger FOV than the original reference
image, the resulting resliced images are off-center (presumably because
the origin is taken as the upper-left voxel). Is there a way for Flirt to
reslice so that the origin is taken as the center voxel for both the input
and reference images?