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Re: [SCIRUN-USERS] [Seg3D] Trouble with BioMesh3d

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  • From: Jess <>
  • To: Bradley Due <>
  • Cc:
  • Subject: Re: [SCIRUN-USERS] [Seg3D] Trouble with BioMesh3d
  • Date: Wed, 25 Jan 2017 22:52:57 -0700

Hi Brad,

This is really a topic for the scirun-users list, rather than seg3d, so I’ve
moved it to that list.

The files for these variables can be located anywhere. The bin directory is
probably not a good location. The model config file should also probably be
saved somewhere else. the model_input_file is the full path to the
segmentation saved as a nrrd file. The model_output_path is the place that
you want to save it. This directory will be made if it doesn’t exist. If
you try to choose a location that lacks the appropriate permissions, it will
cause problems. Also, assuming that you are running on osx or linux, it is
better to run biomesh from the command line than through the app.


> On Jan 25, 2017, at 8:33 PM, Bradley Due <> wrote:
> Hello all,
> I am having trouble getting my segmentation through BioMesh3D so that I can
> run FEM models with my volume from Seg3D. I think the problem my involve
> with the values I am assigning to 'model_input_file' and
> 'model_output_path'. Does the input file and output path need to be in the
> bin/FEMesher directory? Or is there another directory where I should save
> my files?
> When I run step one completes, but prior to starting step 2 I
> get the error message: ('Execution failed with error ',' [Error 2] The
> system cannot find the file specified') child killed: unknown signal.
> Does anyone have any idea as to what the problem could be? Any help would
> be greatly appreciated as this is for my engineering senior capstone
> project.
> Best regards,
> Brad
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