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.
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