[MINC-development] Mincmath crashes during recon-all runing from simnibs mri2mesh MINC

[Andrew Janke]

That error output is from N3 (nu_estimate_np....). It's a guess but
check the input file, this usually means that there isn't sufficient
image data t make a sensible histogram for N3's estimation of B0 bias
field.

An over-zealous mask from a previous image?


a
On Sat, 28 Jul 2018 at 20:40, Russell Butler
<Russell.Buttler at usherbrooke.ca> wrote:
>
> Hello, i am trying to run mri2mesh, a simnibs command that uses freesurfer’s recon-all. however, after less than 2 minutes a crash occurs with the following message:
> Processing:…Done
> ncvarput: ncid 5: Protocol error
> miicv_put: MINC package entry point
> nu_estimate_np_and_em: crashed while running mincmath (termination status=768)
> nu_correct: crashed while running nu_estimate_np_and_em (termination status=768)
> ERROR: nu_correct
> Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux
>
> recon-all -s fs_badger_alex exited with ERRORS at Thu Jul 26 23:59:42 EDT 2018
>
> does anyone know how to resolve this? i’m running it on virtualbox neurodebian.
>
> thanks,
>
> Russell
>
>
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