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Re: [SCIRUN-USERS] Error with BioMesh3D

Chronological Thread 
  • From: Jess <>
  • To: Trevor Aguirre <>
  • Cc:
  • Subject: Re: [SCIRUN-USERS] Error with BioMesh3D
  • Date: Thu, 4 Jan 2018 12:55:51 -0700

Hi Trevor,

It looks like the problem is that you are trying to write the data in a place you do not have permissions to do so.  You should be able to fix this by changing the model_output_path in the file to a location with the correct permissions.  Something like:
Also, the format for the input file might be incorrect too. It should probably be:
Hope that helps


On Dec 23, 2017, at 1:42 PM, Trevor Aguirre <> wrote:


I have a question about using BioMesh3D

I am trying to run through the tutorial for the tooth. I have modified the file to reflect the correct directory for the tooth-seg-unorient.nrrd file as well as modified the for the correct output directory. The tooth-seg-unorient.nrrd and the are in the same folder on my desktop. When trying to run this from cmd.exe I encounter the errors below and in the attached image. 

The first steps are me changing my working directory to reflect the directory where the file is on my computer and then me entering the file path to where tooth-seg-unorient.nrrd and the files are located on my PC. 

It says invalid syntax was encountered in the file at line 262. Do you have any insight on this issue? I am not sure what I have done incorrectly so any insight would be much appreciated. I have attached my file if it is need. 

Begin error message

C:\>cd Program Files\SCIRun 4.7\bin\FEMesher
C:\Program Files\SCIRun 4.7\bin\FEMesher>
default binary_dir = C:\Program Files\SCIRun 4.7\bin
Model configuration file is needed to run meshing pipeline.
Which model configuration file to use?  C:\Users\aguirret\Desktop\Tooth\
Traceback (most recent call last):
  File "C:\Program Files\SCIRun 4.7\bin\FEMesher\", line 262, in <module>
  File "<string>", line 77
    ags available in this option are the same as the previous variable. It
SyntaxError: invalid syntax

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Program Files\SCIRun 4.7\bin\FEMesher\", line 265, in <module>
  File "C:\Program Files\SCIRun 4.7\bin\FEMesher\", line 87, in write_error
    txt_file = open(stage_path, 'w')
PermissionError: [Errno 13] Permission denied: '.\\mesh_state.txt'

End error message

Best regards and looking forward to your reply,

Trevor G. Aguirre
PhD Student, Mechanical Engineering, Colorado State University
Graduate Research Assistant, Orthopaedic Bioengineering Research Laboratory
National Graduate Representative, Society of Hispanic Professional Engineers

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