[Simnibs-discuss] mri2mesh error

Axel Thielscher axelt at drcmr.dk
Wed Dec 9 17:37:28 CET 2020


we tracked the error down to the use of Freesurfer 7 instead of 
Freesurfer 6.

mri2mesh uses mris_convert from freesurfer to convert the the freesurfer 
surfaces to .stl-files. Up to version 6, mris_convert wrote ascii 
.stl-files; since freesurfer 7, it writes only binary .stl-files. 
Because meshfix can only read ascii stl-files, it crashes.

So, for now, the work around is to use Freesurfer 6.0.1...

Hope this helps.

Best regards,


On 12/9/2020 5:27 PM, Smyk, Nathan wrote:
> Good morning Valerie,
> This is a long shot e-mail! My name is Nate Smyk, and I’m working at 
> the University of Pennsylvania in neuroimaging, and I am having the 
> same issue with Simnibs that you had reported here: 
> https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html 
> <https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html>. 
> I saw Axel responded saying Mac Catalina might be the issue (which I 
> am also running on now). Did you happen to find a fix for this fseek 
> issue? Any insight would be GREATLY appreciated!!!
> ERROR- fseek
> /Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335
> failed.exiting mri2mesh after error
> Best,
> Nate Smyk
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby

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