[MINC-users] Problems with mri_nu_correct.mni

[Emmanuelle Renauld]

   ​

   Hi,

   I have just installed FreeSurfer, and I have problems running
   recon-all. I think the problem is linked to mni. The error log says
   nothing, only "exited with ERRORS" after running the following line:

                            mri_nu_correct.mni --n 1 --proto-iters 1000
   --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

   If I go in freesurfer/mri/ and run this line, the output says many
   warnings such as

                          defined(@array) is deprecated at
   /usr/local/FreeSurfer//mni/bin/nu_estimate_np_and_em line 165.
                            (Maybe you should just omit the defined()?)
   And then stops while running the following line:
                           nu_estimate_np_and_em -parzen -log -sharpen
   0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify
   -b_spline 1 -distance 50 -quiet -execute -clobber
         -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4145/0/
   ./tmp.mri_nu_correct.mni.4145/nu0.mnc
   ./tmp.mri_nu_correct.mni.4145/nu1.imp
                            Assertion failed at line 827 in file
   templates/CachedArray.cc
                            nu_estimate_np_and_em: crashed while running
   volume_stats (termination status=256)
                            nu_correct: crashed while running
   nu_estimate_np_and_em (termination status=256)
                            ERROR: nu_correct
   I found many threads about similar problems, but none were solved, and
   they were all old. One recommanded adding more memory to the
   VirtualBox, and since it is my case, I did so, but the bug stays. Any
   ideas?
   Thank you very much,
   Emmanuelle