Can you send us the details in the error logs?
We need to see why the brainstem segmentation is failing.
All the best,
On 13 Aug 2009, at 21:33, Buyean Lee wrote:
> Strangely, FIRST ('run_first_all') does not generate the output
> files (both *_all_fast_firstseg.nii and *_all_fast_origsegs.nii) of
> a few MRIs (5/92 MRIs).
> I believe this is due to the fact that FIRST failed to generate
> *_BrStem.* files of those 5 MRIs (this is why it can't run fslmerge
> in the 'run_first_all' script).