> I haven't used Featquery_gui to generate these masks. Instead, I
> created the non-linearly transformed mask manually and then fed it
> into a modified version of the featquery script (i.e. with the
> "applywarp" step deactivated since it had been done already). The
> linearly transformed mask was created by hand with flirt for
> comparison. I had in mind that the default thresold value was 0.5 -
> but that was true in featquery, not in flirt, sorry!
then I understand it. The "problem" is that applywarp will by default
write its output in the same format as the input. Your input file
(mask_standard) is an INT32 file, i.e. can only represent integer
values. Therefore, even though applywarp calculates it correctly, all
values <1 will be set to zero when mask_native_space_non_linear is
written to disk.
You can fix this by
applywarp all_the_stuff -d float
which will force the output to be a FLOAT32 image.
In the featquery script this is taken care of by an explicit
conversion of the mask to float prior to resampling it.
Good luck Jesper