Dear Derek,
It's not clear what the problem might be from this.
Could you create an illustration (e.g. jpg/png/etc) of the problem and post the result on a photo sharing website (i.e. include the link in your reply to the FSL list)?
This will hopefully give us a better idea of what is going wrong.
All the best,
Mark
On 5 Feb 2014, at 20:42, Derek Archer <[log in to unmask]> wrote:
> Hello,
>
> I am doing FLIRT and FNIRT on healthy brains as well as stroke brains. I am able to successfully transform control brains into MNI space. Additionally, I am able to get stroke brains transformed into MNI space. (Using the inmask option.)
>
> The problem I am having is that when I use the inmask option for the stroke brains, there is smearing around areas that are just outside of the inmask, and it occurs in the FNIRT step. (Everything is aligned correctly, though.) Is there a way to correct this? The code I'm using is below:
>
> fnirt --ref=FMRIB --inmask=lesion --in=FA image --config=FA_2_FMRIB58_1mm.cnf --iout=fnirted_brain --jout=jac_sub_to_FMRIB --cout=coef_sub_to_FMRIB
>
> Thanks as always,
> Derek Archer
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