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Hi,
I have just installed FreeSurfer, and I have problems running recon-all. 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. Most recommanded asking directly to MNI, but I found no
such thread on the MINC-users forum. I thought I would check if there has been any update on this issue recently.
Thank you very much,
Emmanuelle
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