23 lines (15 loc) · 1.11 KB

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

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.
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

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
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!