> I ran sienax on a 1x1x1mm T1 whole brain image and while the 'brain' img
> looks fine when overlaid on the original, the 'talmask' img chops off a
> couple of cm from the inferior prefrontal cortex (I have a jpg available
> but I couldn't find out how to attach it). Has anybody come across the
> same problem and (hopefully!) found a way to solve it?
it is worth checking if the orientation of your images corresponds with the
FSL-templates (usually in /usr/local/fsl/etc/standard, e. g. using the
slices-command); I had parts cut off on the resulting render image due to
this - meaning that the obviously segmented red-colored segmented parts did
not cover the whole brain.
MPI of Psychiatry, Munich