run_elastix_settings

#!/bin/bash

# Settings for run_elastix


# When you downloaded elastix from https://github.com/SuperElastix/elastix/releases
# and extracted the contents, where on your computer did you put the extracted folder?
# For example, if you put the folder at ~/software/elastix-5.0.1-linux, then set this 
# variable to be ~/software
elastix_installation_location=~/software


# What is the filename of the template you want to register images to?
# If the file is in this run_elastix folder, just provide its filename.
# If the file is elsewhere on your computer, provide the full path.
template=JRC2018_VNC_FEMALE_4iso.nrrd


# How many parallel threads do you want to allow elastix to run?
# A reasonable number to use here is the number of threads that your computer can run simultaneously minus 1 or minus 2.
# On Linux, you can find the number of threads your computer can run simultaneously by running: nproc
# On Mac, you can find the number of threads your computer can run simultaneously by running: sysctl -n hw.ncpu
# On Windows, you can find the number of threads your computer can run simultaneously by looking at the Performance tab of the Task Manager
number_of_threads_to_use=7  # A reasonable default for a computer that can run 8 threads simultaneously