Freesurfer experts,
I have a few fractional anisotropy images linearly registered to an FA atlas. I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the output is entirely NaNs.
I ran the program in verbose mode--and everything is NaN's. e.g.:
SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan Jacobian range is nan -- nan ***Going to next resolution level*** Setting subsampling Setting reg mode Setting lambda New Lambda: 30 SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan
Is this simply because there are NaN's in the input image? Will replacing them with 0 fix the issue, or will it lead to strange behaviour in FNIRT?
Any help is appreciated.
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003tel:713-363-9003
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