From Russell.Buttler at USherbrooke.ca Fri Jul 27 00:34:37 2018 From: Russell.Buttler at USherbrooke.ca (Russell Butler) Date: Fri, 27 Jul 2018 04:34:37 +0000 Subject: [MINC-development] Mincmath crashes during recon-all runing from simnibs mri2mesh MINC Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.janke at gmail.com Sat Jul 28 08:02:30 2018 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 28 Jul 2018 22:02:30 +1000 Subject: [MINC-development] Mincmath crashes during recon-all runing from simnibs mri2mesh MINC In-Reply-To: References: Message-ID: 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 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 > > > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development