Hi again Martin,
> if the back transformation computed by FNIRT in the first place is
> fine, then I don't really need to bother with invwarp, no?
> I could script the back-warp of the OxfHarv mask for each subject
> with `applywarp`, e.g.
>
> applywarp --ref=example_func_sub1run1 --in=OxfrHarv_ROI --
> warp=sub1run1.feat/reg/standard2example_func.m --out=sub1run1_ROI --
> interp=nn
I am not really sure what you mean here, but I am guessing you refer
to standard2example_func.mat? This is not calculated by fnirt, and is
in fact not a non-linear transform at all. This is calculated by flirt
and is effectively the inverse of the transform compose from
example_func2highres.mat and highres2standard.mat. I you "cat" it
you'll see that it is a text file with a 4x4 matrix.
applywarps expect a non-linear warp as argument to --warp.
If you want to use standard2example_func.mat you should use flirt with
-applyxfm and standard2example_func.mat as argument to -init. But what
you get then is the inverse of the "linear part" of the transform.
Good Luck Jesper
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