ASCENT Troubleshooting Guide
General Troubleshooting Steps
Check your geometry (ascent/samples/sample_index/models/model_index/debug_geom.mph)
Check your sample (ascent/samples/sample_index/slides/cassette_index/slide_index/masks)
Installation Issues
NEURON
issue: Sometimes NEURON installation will complete but NEURON will not be installed
solution: Run the installer in Windows 8 compatibility mode
Pipeline Issues
Sample
issue: Small white pixel islands cause the pipeline to fail, or the pipeline does not fail but very small elements are present as fascicles that reflect segmentation errors
solution: increase value of image_preprocessing>object_removal_area in sample.json
Model
issue: fascicle borders appear ragged/wavy in model geometry
solutions:
Increase inner_interp_tol and/or outer_interp_tol in sample.json (depending on whether the issue exists for outers or inners)
If your mask is very pixelated, increase smoothing>fascicle distance in sample.json
NEURON Issues
Issue: Compiling NEURON files with python submit.py
results in an error, mpicc: command not found
Solution: Install open-mpi 2.0 and add to path
Python Issues
issue: python output prints out of order with java output
solution: pass the -u flag (i.e. python -u run pipeline
), which turns off output buffering