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