-
Notifications
You must be signed in to change notification settings - Fork 749
Description
Is your feature request related to a problem? Please describe.
The starting point for running Auto3DSeg on custom data is to use the tutorials here, but the explanation on building custom Decathlon-style datalist files is lacking.
Describe the solution you'd like
There should be a clear explanation on how to build a custom datalist, right in one of the autorunner notebooks or in the README.
I'm happy to add this.
Describe alternatives you've considered
- An extra notebook could be added that has instructions on running the autorunner on a custom dataset, including steps to create the datalist. -- This will be highly dataset-specific, though, and with information on the datalist format available, most users should be able to write a simple script to create a datalist.
- The run_with_minimal_input file shows a datalist, but does not completely describe it.
Additional context
See also my issue in MONAI.
There is a notebook titled msd_datalist_generator.ipynb
. This notebook can generate a datalist file from an existing Decathlon Datalist. This works, but offers little explanation and depends on the directory structure of the existing Decathlon dataset, which already comes with a datalist.json file. The code there is also quite trivial to implement given a good explanation of the format.