[Simnibs-discuss] mri2mesh error

Axel Thielscher axelt at drcmr.dk
Thu May 7 19:05:36 CEST 2020

Dear Valerie,

thanks for contacting us. It seems that we might have to update meshfix 
to work with Catalina. We'll come back to you. In the meantime, could 
you quickly check whether subcortical_FS.stl looks "normal" (i.e. is a 
closed surface) when you open it in gmsh? (gmsh is also part of 
simnibs). Otherwise, please let us know.



On 5/7/2020 6:48 PM, Valerie Nicolson wrote:
> Hello,
> I am a new simnibs user on a Mac running Catalina 10.15.4. After 
> installation (and verifying the simnibs gui using ernie) I tried 
> creating a mesh using mri2mesh using ernie's T1 only
> mri2mesh --all ernie org/ernie_T1.nii.g
> After many hours and lots of output it crashes. This is the last of 
> the output:
> meshfix subcortical_FS.stl
> ERROR- fseek 
> /Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 
> failed.exiting mri2mesh after error
> I checked, and subcortical_FS.stl exists and is definitely longer than 
> 80 (this seems to be the fseek call in io.cpp that is failing). I've 
> also tried running meshfix on other .stl files and get the same error, 
> so I'm getting the idea that meshfix is trying to open some other 
> file). Any ideas of how to fix this or what file might be missing from 
> my installation?
> Thanks,
> Valerie Cardenas Nicolson
> _______________________________________________
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> Simnibs-discuss at drcmr.dk
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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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