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

Chronological Thread 
  • From: Brett Burton <>
  • To: Bradley Due <>
  • Cc: Brett Burton <>, Jess Tate <>,
  • Subject: Re: [SCIRUN-USERS] [Seg3D] Trouble with BioMesh3d
  • Date: Fri, 27 Jan 2017 10:06:32 -0700


The error you are seeing when running BuildMesh is not likely related to where you have placed the model_config file (on your desktop).  That being said, I would recommend a different location for it, even if it is in a separate folder on your desktop (maybe something like ~/Desktop/Biomesh/). I would also put a separate folder in the Biomesh folder that is just for your output (~/Desktop/Biomesh/output/ or something like that).  The reason is that the output that Biomesh generates can include 90 or more files and folders…you probably don’t want that cluttering your desktop with all that.  I would also not put it in FEMesher, personally.  Put it somewhere that you can find it easily, but where it won't clutter up the folder you are calling your code from.

Moving your input and output locations will require you to edit the input and output calls in your model_config file.  This may be where your error is coming from in the first place. Your "model_input_file=“ needs to point to your segmentation (nrrd file).  Your “model_output_path=“ should point to your output folder.  Here’s an example:


If you are already doing that, then I suspect your error arises because you are not pointing at your model config file, or you have a typo somewhere.

./ /Users/MrIncredible/Research/Experiments/2013/10-24/BioMesh/

But then again, maybe I misread what your error actually was. Double check to make sure BuildMesh is pointing to the model_config file and that your inputs and outputs are pointing to the correct files.  If the error persists, send us the error message and the model_config file.


On Jan 26, 2017, at 12:13 AM, Bradley Due <> wrote:

Hi Jess,

Thank you for replying so quickly. Where should I save the file? Should that be in FEMesher? 

I saved the .nrrd file to the desktop and I set the output path to my desktop as well. I also have the file saved on the desktop. However when I try to run and have the file saved to my desktop I get an error saying that the file cannot be found. Is that an issue with where the file is located or is it another issue?


On Wed, Jan 25, 2017 at 11:52 PM, Jess <> wrote:
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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