Hi,
Call me a little overeager, but I've already been testing out FNIRT.
fnirt --in=anat.nii --ref=MNI152_T1_2mm_brain.nii.gz
--refmask=${FSLDIR}/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
--aff=flirt_anat_to_MNI.mat --cout=fnirt_anat_to_MNI_transf
--config=T1_2_MNI152_2mm
The result looks quite good, except for a noticeable "indentation" in
the normalized result (see cross hair in attached images). The edge of
the warped brain in one location in parietal lobe
is approximately 1cm inside the edge of MNI template. In contrast,
the edge using 12 dof flirt normalization on the same brain is quite
close to the MNI edge in this location (although other aspects of the
alignment, are not as good as with FNIRT).
I tried adjusting "warpres" both up (12,12,12) and down (7,7,7) but
got similar results. Is there an FNIRT parameter that can be tweaked
to improve edge alignment in these kind of cases?
thanks,
Brad Buchsbaum
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