DeepSeg Runtime Estimation

This repo acts as a means to evaluate the runtime of the deepseg utility provided by the Spinal Cord Toolbox, allowing users to estimate the approximate time required to run an analysis.

Requirements

• Python 3.7 or newer
• A working installation of Spinal Cord Toolbox

Preparing to run

1. Find and copy the path to your SCT install bin (i.e. /user_name/spinalcordtoolbox/bin); this path will be referred to as sct_bin_path from here on.
   • If on Linux/macOS, you can find this with the which sct_testing command.
2. Run setup.py -s {sct_bin_path}.
   • This downloads a file, and resamples it a number of times to standardize our estimates. This can take a while!

Running the tool

1. Decide on the deepseg task you want to evaluate; this is denoted as the task_id in code snippets below.
   • You can get a list of available tasks by calling sct_deepseg -list-tasks
2. Run run.py -s {sct_bin_path} -t {task_id} and let it complete
   • How long this takes depends substantially on the model being used; be patient!