Common Issues

Common issues with ViNERS

This list was last updated 26 November 2021

Problem: During a call to models.nerve_anatomy (in the mesh_generation subfunctions), you receive error messages from GMSH followed by a MATLAB error, resembling the following:

Error   : Invalid boundary mesh (overlapping facets) on surface 1295 surface 1256
Error   : No elements in volume 61 62 63 64 65 66 859 861 862 864 865 866 867 868 869 870 871 872 873 874 875 
Info    : Done meshing 3D (Wall 1.63169s, CPU 1.5625s)
Info    : 50040 nodes 105581 elements
Error   : ------------------------------
Error   : Mesh generation error summary
Error   :     0 warnings
Error   :     2 errors (or more)
Error   : Check the full log for details
Error   : ------------------------------
Info    : Writing 'C:\Users\user\AppData\Local\Temp\pn-mdl-21080\nerve+array.msh'...
Info    : Done writing 'C:\Users\user\AppData\Local\Temp\pn-mdl-21080\nerve+array.msh'
Info    : Stopped on Thu Nov 25 22:24:55 2021 (From start: Wall 13.1811s, CPU 12.875s)
Reading "C:\Users\user\AppData\Local\Temp\pn-mdl-21080\nerve+array.msh"
 ...
Error: Index in position 2 exceeds array bounds.
...
Error in
models.nerve_anatomy>generate_nerve_mesh (line 572)
  m = mesh.make_gmsh_thinLayer(PN_mesh('.geo'), e.Perineurium_mm );
Error in models.nerve_anatomy (line 75)
  m = generate_nerve_mesh(get_,named, e);

Solution: This is most often caused by bad mesh geometry (e.g. a fascicle clipping through the electrode array). To visualize the input geometry for the mesh, cd(tools.cache) (see +tools.cache, then open nerve+array.geo in GMSH to view the generated input geometry to the mesh.

Most commonly, this issue is corrected by adjusting the -xMove / -xScale / -xRotate inputs to mesh.insert_gmsh_fascicles. The +plot utility +plots.preview_fascicles is also helpful here.

Problem: tools.cache('reset')

Error using rmdir: No directories were removed.
Error in tools.cache (line 67): rmdir(cachepath,'s');

Solution: Close any open files (e.g. a .geo file open in GMSH) and ensure that the MATLAB working directory is not in the directory you’re trying to remove (i.e. pwd is not in C:\Users\user\AppData\Local\Temp\pn-mdl-*\) before calling tools.cache.

Problem: Unrecognized function or variable 'ctfroot'. Error in tools.file (line ...)

Solution: This is an obsolete test to see if ViNERS is running in MATLAB or OCTAVE. If you are running MATLAB, replace isempty(strfind(ctfroot,'MATLAB')) %#ok<STREMP> with false. If you are running OCTAVE, replace isempty(strfind(ctfroot,'MATLAB')) %#ok<STREMP> with true. This issue can also be solved by installing the MATLAB compiler toolbox, or replacing with a call to tools.isOctave.

Problem: Error using tools.parse_arguments (line 132) expected positional argument 2: axons Error in models.axon_thresholds (line 35) % most other modules are similar to this [EM,AX] = tools.parse_arguments(varargin, 'LOAD', ...

Solution: Most model components require both an EIDORS fields definition file (either a sensitivity or a [stimulus] (Data/eidors_stimulus.mat) file and an axon population definition file.

In this example, I got this error with a call to models.axon_thresholds(opts,'-file', eidors_file). I was able to fix this issue by either defining opts.thresholds.axons = axons_file, or by changing the call to models.axon_thresholds(opts,'-file', eidors_file,'-axons', axons_file), or by changing the call to models.axon_thresholds(eidors_file, axons_file, opts). See also +tools.opts_to_args.

Problem:

Error using eidors_obj. 
Error in function test_install (line 145)
EIDORS not correctly started. Did you do ">>run /path/to/eidors/startup"? 

Solution: Something went wrong starting EIDORS. Try running tools.setupEIDORS. That should produce the following output:

EIDORS:[=== SETTING UP EIDORS version 3.9.1 ===]
EIDORS:[tested function eidors_var_id: OK]
 EIDORS:[Setting Default Colours]
EIDORS:[Installed EIDORS (Ver: 3.9.1)]
EIDORS:[Parameter: cache_size=1024 MB]
EIDORS:[Parameter: mapped_colour=127]
EIDORS:[Default background colour: white]
EIDORS:[EIDORS mex folder: C:/Users/user/Documents/MATLAB/EIDORS/eidors/arch/matlab]
EIDORS:[EIDORS cache folder: C:/Users/user/Documents/MATLAB/EIDORS/eidors/models/cache (must be writable)]
EIDORS:[EIDORS model cache: C:/Users/user/Documents/MATLAB/EIDORS/eidors/models/cache]
EIDORS:[New to EIDORS? Have a look at the Tutorials.]

If that output does not appear, try running eidors_startup, which should be located in the folder returned by tools.configuration('eidors') (see tools.configuration. If that fails still, tools.fix_eidors_overloads (new) is sometimes necessary depending on the versions of MATLAB and EIDORS (note: this modifies the EIDORS source code, please only run once). global eidors_objects may also give some insight into what is happening here.

Common issues with ViNERS experimental code

(note: this is largely peripheral to ViNERS itself, but is included here for completeness. Some of the solutions to these problems )