I have a problem with fnirt when using it to register two anatomical images
with small volume for refmask such as hippocampus mask. When I run the
command with the following options:
fnirt in image1 ref image2 ioutimage3 refmask=ref.nii.gz config file T1_2mm
and affine initial matrix.
It sticks in a loop and doesn't register two images even after a day. I'm not
sure that this problem occurs when using small refmasks since I had the same
problem sometime using larger refmasks.